Multiz Alignments of 20 Vertebrates

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Alignment block 1 of 66 in window, 80055139 - 80055161, 23 bps B D Rat ttgaaaagtt---cccactctgtgct B D Mouse ttaaaacgtt---ctcactatctgcc Prairie vole ttaaaagact---ctcactatgtgcc B D Guinea pig ttgcaaggtcaagctcagccccagca B D Chimp ttaaatagct---ctcactgtgtgct B D Panda ttcgatagca---ctcactgtgggcc B D Cat --caatagca---ctcactgagtgcc B D Cow ttccatagca---ctcactctgtgcc B D Dog ========================== B D Rabbit ========================== B D Rhesus ========================== B D Human ========================== B D Opossum ========================== B D Chicken ========================== B D X. tropicalis ========================== B D Platypus ========================== B D Tarsier ========================== Inserts between block 1 and 2 in window B D Mouse 7bp Prairie vole 7bp B D Chimp 8bp B D Panda 8bp B D Cat 8bp B D Cow 10bp Alignment block 2 of 66 in window, 80055162 - 80055206, 45 bps B D Rat ttttaggatccctatgaaatcgac-gatgtc----actg----accccattttg B D Mouse ttttaggatccctatgaaatcaac-gatatcagtgactg----tccccattttg Prairie vole ttctaggatccctatgaagtcaac-aatgtgagtgaatg----tccccattctg B D Guinea pig atttagtgacttagaaagattgaa-aaaaa-----aat-----------tttta B D Chimp ttctaggaaccatttaggggaggg-actgccaatacatg----accccatttta B D Dog ttctaggagccctataggaatgaggacagtc----aatg----gctccatttca B D Panda gtctaggaaccctgtaggaataggcactatc----gatg----gctccctttca B D Cat ttctaggagccttatggggatagg-actgtc----gatggctcgctccatttca B D Cow -tctaggaacccctatggagtggggactgac----aatg----gttccattttg B D Rabbit ====================================================== B D Rhesus ====================================================== B D Human ====================================================== B D Opossum ====================================================== B D Chicken ====================================================== B D X. tropicalis ====================================================== B D Platypus ====================================================== B D Tarsier ====================================================== Alignment block 3 of 66 in window, 80055207 - 80055222, 16 bps B D Rat aag-----atga-ggaaa--ctga B D Mouse aag-----atga-ggaag--ctga Prairie vole cag-----atga-ggaaa--ctga B D Guinea pig aaggggtaatgatggtgg--ctta B D Chimp cag-----atga-ggaaatg---- B D Tarsier ----------aa-gaaaa------ B D Dog cag-----ataa-ggaaa--ctaa B D Panda cag-----atga-ggaaa--ccga B D Cat tag-----atga-ggaaa--ctaa B D Cow cag-----atga-ggaaa--ccga B D Rabbit ======================== B D Rhesus ======================== B D Human ======================== B D Opossum ======================== B D Chicken ======================== B D X. tropicalis ======================== B D Platypus ======================== Alignment block 4 of 66 in window, 80055223 - 80055259, 37 bps B D Rat gtcccaaagaggttaag-aagttagtccaacta------------aggtg--------- B D Mouse gtcccaaagaggttaag-aagttagtccaacta------------aagtg--------- Prairie vole gtcccagagaagttaagaaaactatgccaacta------------agatg--------- B D Guinea pig gctcagggtgaagaaag-aaattagtctgaggt------------gaggt--------- B D Rabbit gtctcacgtgggtcagg-aggc-agcagtatgc------------aaatg--------- B D Chimp ggctcagagaggttaag-aaactagtccaggcc------------gggcg--------- B D Tarsier ----aagaaaagaaaag-caactagtctaaggctgcaatccaaatggatg--------- B D Dog ggcaca-gaaggttaag-aaactagtccaaggtcacactcc----aagtggctgatgtg B D Panda ggcacagggaggttaag-aaattagtccaaggtcacactcc----aagtggctgaggtg B D Cat ggcacagagaggttaag-acactagtccaaggtcacactcc----aagtggctgaggtc B D Cow ggcacagagaag--atg-aaattagtttaaggtcata--cc----aagtggctgaggt- B D Rhesus =========================================================== B D Human =========================================================== B D Opossum =========================================================== B D Chicken =========================================================== B D X. tropicalis =========================================================== B D Platypus =========================================================== Inserts between block 4 and 5 in window B D Chimp 881bp B D Tarsier 11bp Alignment block 5 of 66 in window, 80055260 - 80055332, 73 bps B D Rat ------gatcctaaac-----------------------acagtat-ctgaatggcagcaaagcaatgtt B D Mouse ------gatcctaaac-----------------------acagtat-ctgaatggcacc----------- Prairie vole ------gatcctaagt-----------------------acaatat-ctaaa----------acaatgct B D Guinea pig ------gagactaaac-----------------------acagtat-ctggaaggcagtatagtgctgtg B D Rabbit ------agccctg--------------------------atgcttt-ctagg-agaagtacagccagtcc B D Tarsier ------gaactcagacaata---------------tttaactgact-ctgggaggcaatatagagatatt B D Dog ggatttgaactcagagggtaagtattcaaatga--ctggatgcttt-ctgtgaggcaatatagagatgtt B D Panda ggatctgaattcagggggtaagtcttcaaatga--ctggatgcttt-ctgggaggcaatatagagatgtt B D Cat ggatatgaactcgaggagtagggattcaaacgactctggatgccccaaagggaggcaatacaaagatgtg B D Cow ggatttgaagtcaggcaatg----ttcaaatgactctcaatgcctt-ctggggagcaatatag------- B D Rhesus ====================================================================== B D Chimp ====================================================================== B D Human ====================================================================== B D Opossum ====================================================================== B D Chicken ====================================================================== B D X. tropicalis ====================================================================== B D Platypus ====================================================================== Rat ataccactaattctgaagccaacct---tcttggat Mouse acaccactaattctgaagccaacct---tcttggat Prairie vole tcatcacccactctgaagccaa------gcttgaat Guinea pig gtgccacttgtt----agctg----------tggaa Rabbit cagccgccagctctggagctaacct-aagcttgggt Tarsier acagccccagctctgaagccaacct---gcttggca Dog cttgtgccagctctggaatcaacctgaagtttgggt Panda attgtaccagctctggagccaacctgaaattcgggt Cat gttgtgccagctctggagccaacctgaaactt---- Cow --------agctctggagccaaacc---atttgggt Rhesus ==================================== Chimp ==================================== Human ==================================== Opossum ==================================== Chicken ==================================== X. tropicalis ==================================== Platypus ==================================== Inserts between block 5 and 6 in window B D Tarsier 4bp Alignment block 6 of 66 in window, 80055333 - 80055342, 10 bps B D Rat ------------tttaatt-----------tca B D Mouse ------------tttaatt-----------cta Prairie vole ------------tctaact-----------tca B D Guinea pig ------------cctatgg-----------caa B D Rabbit ------------tccagccctggtctcccactg B D Rhesus ------------tctacta-----------ttt B D Tarsier ------------tctaccc-----------ttt B D Dog tgaaaccctaggtatacca-----------ttt B D Panda tgaaaccctgggcaaacca-----------ttt B D Cat ----------ggtatatca-----------ttt B D Cow tgaa------agcatacca-----------ttt B D Chimp ================================= B D Human ================================= B D Opossum ================================= B D Chicken ================================= B D X. tropicalis ================================= B D Platypus ================================= Alignment block 7 of 66 in window, 80055343 - 80055440, 98 bps B D Rat accagctgtgg--gatttggaca-aaatacaata---------acttcagtttcctcatctg-ataatgg B D Mouse attagctgtgg--gacttggaca-aaatgtaaaa---------acttcagtttcctcatctgtatagtgg Prairie vole atagaatat----cccctgg-----------------------gcctcaatttccccatttgtatagcgg B D Guinea pig aacgtataaca--tctctgg-----------------------gccttagtttcactatctgtg----gc B D Rabbit accagctgcaagctccctgg-----------------------gccccggcctccccacctgcacattga B D Human attatctgtag--gatttgtgca-atgtgtataacctctctgagcctcagtttccccatctgcataatga B D Chimp attatctgtag--gatttgtgca-atgtgtataacctctctgagcctcagtttccccatctgcataatga B D Rhesus attatctgtag--gatttgtgca-atgtgtataacctctctgagcctcaatttccccatctgcataatga B D Tarsier attagct-tag--gatttgggcatacgtgtgtaacctctctgggcctaagtttccccatccacaccatga B D Dog attagctgtgg--gatttgggta-aaatgcctaactgctctgctcctcagttt--ccatatgcagagtga B D Panda ataagttgtgg--gatttgggca-aaatgcctaactgctccggtcctcggttt--ccat-cgcacagtga B D Cat atgagc-----------tgggca-aaatgcttaactgctctgggcctcagtttccccatttgcatagtga B D Cow attggctgtgg--gatttgggca-aaatgcctaactattctgggtgtcagtttcctcatctacacaatga B D Opossum ====================================================================== B D Chicken ====================================================================== B D X. tropicalis ====================================================================== B D Platypus ====================================================================== Rat agatcatatcagttctgat---------ctcactagacagtacattgctt Mouse agattatattagttcagac---------ctcaccagagagtacactgctt Prairie vole agatcatattacttccgac---------ctcactagacaatacattgctg Guinea pig atctcacactggctctcat---------cacctggggctgcctattgctt Rabbit agatcttactgaccc-------------ctcacggggctgtttgctgctt Human agatcatattggtacccac---------cttatagggctgtctgttgcct Chimp agatcatattggtacccac---------cttatagggctgtctgttgcct Rhesus agatcatattggtacccac---------cttaaagggctgtctgttgcct Tarsier aaatcatattggtacccac---------ctcaaagggctgtttgttgctt Dog ggattacattggtactcac---------cccacagagctgt--------- Panda ggatcacatcggtgctcac---------ctcatagagctgt--------- Cat ggatcacattgttacgcac---------ctcatgaaacagt--------- Cow agatcagattggtacccacctcgttaggctcatagggctgt--------- Opossum ================================================== Chicken ================================================== X. tropicalis ================================================== Platypus ================================================== Inserts between block 7 and 8 in window B D Rabbit 125bp Alignment block 8 of 66 in window, 80055441 - 80055487, 47 bps B D Rat ctgccta-gtatagggtaaaagtttggt------------gggggt-------cgtatagtgtggga B D Mouse ctgccta-atataggataata-tttagt------------gggggt-------cgtatagtgcggga Prairie vole -taccta-atatcaagcaagcgtttggtggga--------gggagt-------tgtatagtttggga B D Guinea pig gtcccta-gcacacactcaggtttgggt------------agaagtgcagctgctggttatgtgaga B D Human atgccta-gcacacagtaagcttttggtgggggcattaaggggggc-------agtacagcctggtg B D Chimp atgccta-gcacacagtaagcttttggtgggggcattaaggggggc-------agtacagcctggtg B D Rhesus atgccta-gcacatagtaagcttttggtgggggcattaaggggggc-------agtacagcctggtg B D Tarsier gcaccta-gcacatagtaagtttttggtgggagcaggaagacgggc-------agtacatcctggtg B D Dog -tgccta-gcacacactcagcttttg---------------ggggc-------cgtacagag----- B D Panda -tgcata-ccacacagtaaactttt-----------------gggc-------ggtacagag----- B D Cat -tgtcta-gcacatagtaaactttgg---------------ggagc-------agtacagaa----- B D Cow -tgctgatgcatataataagattggggg------------aggcgc-------agtatagag----- B D Rabbit =================================================================== B D Opossum =================================================================== B D Chicken =================================================================== B D X. tropicalis =================================================================== B D Platypus =================================================================== Inserts between block 8 and 9 in window B D Human 1bp B D Chimp 1bp B D Rhesus 1bp B D Tarsier 1bp Alignment block 9 of 66 in window, 80055488 - 80055517, 30 bps B D Rat tttgtgcaccaccaaga-aatct--agtctggt B D Mouse tttgtgtaccaccaagagaatct--agtcaggt B D Guinea pig -------------------ttctagagtcagat B D Human tttgt-taccagcat-ggagtctagagtccgat B D Chimp tttgt-taccagcat-ggagtctagagtccgat B D Rhesus tttgt-tttcagcatgggagtctagaatccgat B D Tarsier tttgt-tactagcatgggactctagagtcagat B D Dog ---------------ggcaatac--ag--ttgt B D Panda ---------------agcaatac--agcctagt B D Cat ---------------ggcagtac--agcctggt B D Cow ---------------ggcagt----ggtctggt B D Rabbit ================================= Prairie vole --------------------------------- B D Opossum ================================= B D Chicken ================================= B D X. tropicalis ================================= B D Platypus ================================= Inserts between block 9 and 10 in window B D Dog 30bp B D Panda 1bp B D Cat 38bp B D Cow 3bp Alignment block 10 of 66 in window, 80055518 - 80055523, 6 bps B D Rat tcaccc--- B D Mouse tcacct--- B D Guinea pig taa------ B D Human taa------ B D Chimp taa------ B D Rhesus taa------ B D Tarsier gaa------ B D Dog tag---ctc B D Cow tag---cag B D Cat ========= B D Rabbit ========= Prairie vole --------- B D Opossum ========= B D Chicken ========= B D X. tropicalis ========= B D Platypus ========= B D Panda ========= Inserts between block 10 and 11 in window B D Dog 138bp Alignment block 11 of 66 in window, 80055524 - 80055590, 67 bps B D Rat ------------------------accaccactactcccccacacacacccccaacacacgcacacactc B D Mouse ------------------------gccgctgcag--ccaccaccaccaccactcccctacccgcctactc B D Guinea pig ------------------------------------ctcctgtgaaaaccccag---------------- B D Human ------------------------------------ctccagtcagagccccag---------------- B D Chimp ------------------------------------ctccagtcagagccccag---------------- B D Rhesus ------------------------------------ctccagtcattgccccag---------------- B D Tarsier ------------------------------------ctccagtcagaggcccag---------------- B D Panda gttaccaacgtgggcctc----tcg-----------attcaggttagctcc------------------- B D Cow --------aatagagctcctattag-----------ctccaggcagacccccag---------------- B D Cat ====================================================================== B D Dog ====================================================================== B D Rabbit ====================================================================== Prairie vole ---------------------------------------------------------------------- B D Opossum ====================================================================== B D Chicken ====================================================================== B D X. tropicalis ====================================================================== B D Platypus ====================================================================== Rat cccatccctgcccccc-acccc- Mouse cccatctctgtcccccgacccc- Guinea pig ----------------------- Human ----------------------- Chimp ----------------------- Rhesus ----------------------- Tarsier ----------------------- Panda ----------------------- Cow ----------------------c Cat ======================= Dog ======================= Rabbit ======================= Prairie vole ----------------------- Opossum ======================= Chicken ======================= X. tropicalis ======================= Platypus ======================= Inserts between block 11 and 12 in window B D Guinea pig 1bp B D Human 1bp B D Chimp 1bp B D Rhesus 1bp B D Tarsier 1bp Alignment block 12 of 66 in window, 80055591 - 80055591, 1 bps B D Rat c B D Mouse c B D Dog c B D Panda a B D Cat = B D Guinea pig = B D Rabbit = B D Rhesus = B D Cow - B D Chimp = B D Human = Prairie vole - B D Opossum = B D Chicken = B D X. tropicalis = B D Platypus = B D Tarsier = Alignment block 13 of 66 in window, 80055592 - 80055604, 13 bps B D Rat atcagatccctag B D Mouse atcagatcact-- B D Dog atcggattccccg B D Panda gtcagagtcccag B D Cat gtcagagccccag B D Guinea pig ============= B D Rabbit ============= B D Rhesus ============= B D Cow ------------- B D Chimp ============= B D Human ============= Prairie vole ------------- B D Opossum ============= B D Chicken ============= B D X. tropicalis ============= B D Platypus ============= B D Tarsier ============= Inserts between block 13 and 14 in window B D Dog 31bp B D Panda 1bp B D Cat 1bp Alignment block 14 of 66 in window, 80055605 - 80055653, 49 bps B D Rat tctgcctcc----tggctgttt-tggg------------atctt-------------------------- B D Mouse tctgcctcc----tggctgttt-tggg------------atctt-------------------------- Prairie vole actgcctcc----tggctgttc-cggg------------atctt-------------------------- B D Guinea pig tctgccctt----tacctcctt-tggg------------atctt-------------------------- B D Human tcctcctct----tagcttctt-tggg------------atctt-------------------------- B D Chimp tcctcctct----tagcttctt-tggg------------atctt-------------------------- B D Rhesus tcctcctct----tagctcctt-tggg------------atctt-------------------------- B D Tarsier tctgcttc------agctgctt-tggg------------agctt-------------------------- B D Dog tctgtgtct----------ctcatgagaaaacaaatacaatcttaaaaaaaaaaaaaaaaaaaaaaaaaa B D Panda tctgcgtct----tagctgcttgtggg------------atctt-------------------------- B D Cat tctgcgtcttagttagttgctcgaggg------------atctt-------------------------- B D Cow tctgc----------------------------------cactt-------------------------- B D Rabbit ====================================================================== B D Opossum ====================================================================== B D Chicken ====================================================================== B D X. tropicalis ====================================================================== B D Platypus ====================================================================== Rat --------tggtgcctg----agttcc--atttcct Mouse --------cggagcctg----agttcc--atttcct Prairie vole --------agatgcctg----agttcc--atttcct Guinea pig --------ggacagcaggtctacttcccggtttcct Human ---gaacaggattctta----tttccc--attccct Chimp ---gaacaggattctta----tttccc--attccct Rhesus ---gaacaggatgctta----tttccc--attccct Tarsier ---gaacaggatggctg----tttccc--attccct Dog aaaaaaaagaatgccta----gttcca--ataccct Panda ---gggcagaatgccta----tttcct--gttccct Cat ---gggcagaatgccta----gctctt--attccct Cow ---gggcaggataccta----tttcct--attcatt Rabbit ==================================== Opossum ==================================== Chicken ==================================== X. tropicalis ==================================== Platypus ==================================== Alignment block 15 of 66 in window, 80055654 - 80055692, 39 bps B D Rat gacagactggggaaagga-----agttgggggttgaaaataaaa- B D Mouse gacaaactggggaaagga-----agttgggggttgacaataaaa- Prairie vole ggaaggttggggaaagga-----gtttagggattggaaataaga- B D Guinea pig agcgggctgggagtgggggcgttggtcagaacctagagataaga- B D Rabbit gtcagcgctgggagagga-------------------gacgggg- B D Human ggagggctaggg-----------ggtcagggactggaggtgggt- B D Chimp ggagggctaggg-----------ggtcagggactggaggtgggt- B D Rhesus ggagggctaggg-----------ggtcagggactggaggtgggt- B D Tarsier ggcggaccgggg-----------agtcgggcatcggaggtgggg- B D Dog ggcaggctgctg-----------ggtcagaggtgggaggtggag- B D Panda ggcaggctgcgg-----------ggtcaggagttagatgtgcgg- B D Cat ggcaggctgcca-----------ggtcagggcttggaggtgggg- B D Cow gatgggctgtgg-----------ggtcaggagttagaggtggggt B D Opossum ============================================= B D Chicken ============================================= B D X. tropicalis ============================================= B D Platypus ============================================= Alignment block 16 of 66 in window, 80055693 - 80055694, 2 bps B D Rat c------c B D Mouse c------c Prairie vole c------t B D Guinea pig tgagacac B D Rabbit c------c B D Human c------c B D Chimp c------c B D Rhesus c------c B D Tarsier c------c B D Dog c------c B D Panda c------c B D Cat c------c B D Cow c------c B D Platypus c------c B D Opossum ======== B D Chicken ======== B D X. tropicalis ======== Alignment block 17 of 66 in window, 80055695 - 80055865, 171 bps B D Rat ctttacctttctcacttggagattgccaggactacctgggggtcgtacaatcaacaagggacgcagaaaa B D Mouse ctttacctttctcacttggagattgccagaactacccgggggtcgcacaatcaataagggacgcaggaaa Prairie vole ctttacctttctcacttggagattgccaggactacccgggggtcgcacaaccaacaggggacgcaggaaa B D Guinea pig ctttacctttctgacttgaagattgccggggctacctggggttcgcacaatcaacagaggacgcaggtaa B D Rabbit tcgtacctttctgacttggagactgcccggagtgcccggggctcgcacaacaagcagcggtcgcaggaaa B D Human ctttacctttctgacttggagatttcccgggctgcccggggttcgcacaaccagcagggggcgcagataa B D Chimp ctttacctttctgacttggagatttcccgggctgcccggggttcgcactaccagcagggggcgcagataa B D Rhesus ctttacctttctgacttggagatttcccgggctgcctggggttcgcacaaccagcagggggcgcagataa B D Tarsier ctttacctttctgacttggagattgcccgggcttccaggggttcgcacaaccagcagggggcgcagataa B D Dog ctttacctttctgacttggagattgccggggctgcccggggtccgcacaaccagcagggggcgcagataa B D Panda ctttacctttctgacttggagattgccggggctgcccggggtccgcacaaccagcagggggcgcaggtaa B D Cat ccttacctttctgacttggagattgccggggctgcccggggtccgcacaaccagcagggggcgcaggtaa B D Cow ttttacctttctcacttggagattgcccgggctgcccggagtccgtacaaccagcagagggcgcaggaaa B D Opossum ccttacctgccggaccttcgagttcccaggactgcctggtgtcctttcaaccagtaggggctggaggtac B D Platypus cctcacctgtcggacgcgcaggttcccggggctgcccgggctccgctcgaccagcagcggccgcaggtac B D Chicken ====================================================================== B D X. tropicalis ====================================================================== Rat gttccccagagacgctgtggatccagctgccctaccacaagccgcagcttggcttctgaaaggcttccga Mouse gttccccagagacgctgcggatccagctgccctaccaccagccgcagcttggcttctgaaaggcttccga Prairie vole gttccccagagacgctgcggatccagctgccctaccaccctccgcagcttggcttctggaaggcttccaa Guinea pig gtaacccagagccgctgcggatccagctgatccaccaccttccgcagcttggcttctgggaggtttccaa Rabbit gtgccccagaggcgctgcaggtccaactgccccaccaccctccgcagccgggcctccgggagacttccgg Human gtgctccagagacgctgtggatccagttgtcccaccaccctccgcagccgggcttcggggaggcttccga Chimp gtgctccagagacgctgtggatccagttgtcccaccaccctccgcagccgggcttcggggaggcttccga Rhesus gtgccccagagacgctgtgggtccagttgtcccaccaccctccgcagccgggcttcgggaaggcttccga Tarsier gtgccccagagacgctgcgggtccagttgtcccaccaccctccgcagctgggcttcggagaggcttccga Dog gtgttccagagacggtgtgggtccagttgccccaccacccgccgcagccgggcttcggagaggcttccga Panda gtgttccagagacggtgtgggtccagttgccccaccaccctccgcagccgagcttcggggaggcttccga Cat gtgttccagagacggtgtgggtccagttgccccaccaccctccgcagccgggcttcagggaggcttccga Cow gtgttccagagacggtgagggtccagttgccccactaccctccgcacccgagcttcggggaggcttccga Opossum ttgccccagaggcgctgggggtccagctgtcctagcagcgtccgaaggtgggcttcagggaggcttcggc Platypus gtgccccagagacgccgcgcatccagctggctcaggaactgctgcaaccgggcccgaggaagactgcgg- Chicken ====================================================================== X. tropicalis ====================================================================== Rat tcagcgggacctt---ggttgggaaa---tgggatgg Mouse tcagcgggacctt---ggttgggaaa---tgggatgg Prairie vole tcagcgcggcctt---ggtagggaaa---tgagatgg Guinea pig ccagcggagccttgggggttggtaaa-------acgg Rabbit tcagcggcgtcta-----------------------a Human tcaatgggacctt---gggaaggagg---tgggatag Chimp tcaacgggacctt---gggaaggagg---tgggatag Rhesus tcaacgggacctt---gggaaggagg---tgggatag Tarsier tcaacggggcctt---gggagggagg---tgggatgg Dog tcaagcggccctt---aggaggagggagcaaggagag Panda tcaaccggccctt---gggagggaat----aggatag Cat tcaaccggccctt---gggagggggg---taagatag Cow tcaaagggccctg---aggaagcagg--------tag Opossum cagggggggcctg---agcctgggaa---gagaacag Platypus --agctggagcgg---ggagggggga---atcgatcc Chicken ===================================== X. tropicalis ===================================== Alignment block 18 of 66 in window, 80055866 - 80055957, 92 bps B D Rat gggaaagaaaa---------atgaaaaaga---------tcccattcccaacttatcccggacgcggttg B D Mouse gaaaaagaaaa---------atgaaaacaa---------ccccattcccaccttatcctgggcgccgttg Prairie vole ggaaaagaaaa---------atgaagacaa---------ccccattcccaccctttcaggggcgacgttg B D Guinea pig gaagagaaaat---------aagaacaatc---------cctcattccgaccctaccccggacgccggtg B D Rabbit agaagagaaga---------atgag---------------cgcactgctccct----------------- B D Human ggaagggaaga---------atgagagcaa------cccccccatttcaaccctaccccgggcgccgtca B D Chimp ggaagggaaga---------atgagagcaa-------ccccccatttcaaccctaccccgggcgccgtca B D Rhesus ggaagggaaga---------atgagagcaa-------cccaccatttcatccctaccccgggcgccgtca B D Tarsier ggaagagaaga---------atgagagcaacccccgccccgccattccaaccctactccgggcgccgctg B D Dog ggaagagaagaaccgaac--gtgagggcaa--------cccccattccaaccctaacccggacgccatcg B D Panda ggaagagaagagccgagc--gtgagagcaa--------cccccattccgaccctaacccggtcgccatcg B D Cat ggaagagaagtgcagagc--atgagaacaa--------cccccataccgaccctaccccggaggccacct B D Cow ggaagagaagagcagagc--atgaaaacga--------ccctcgttccaaccatatcctggaggctgcc- B D Platypus -----------atcaatcatatttgatcaa----------tcaatctccctctagactctaagttcgctg B D Opossum ====================================================================== B D Chicken ====================================================================== B D X. tropicalis ====================================================================== Rat -cccactaggaatgctgattcttcttggtgatgc------agtctc--c Mouse -cctactaggagtcctggctcttcctggtaatgc-----aaatctc--c Prairie vole cccccctagaatccctgactcttcttggcgatgcatcaaaaacttg--a Guinea pig --ccgccatgtgcccgggatcct-ttgggaatga----gcagcctc--c Rabbit -ccccccaaaagcccgggtgcctct----aaggc----gcagcctccgc Human -cccgcgaggagccccgggttctcttcctaatct----gccgcctc--c Chimp -cccgcgaggagccccgggtcctcttcctaatct----gccgcctc--c Rhesus -cccacaagcagccccgggtcctctttctaattt----gcggcctc--c Tarsier -cacccaagtctcctcggttcctcttcgtaatct----gcggcctc--c Dog -cacctaagaagccccggttcttcttcctaattc-----gaacctc--c Panda -cccctaagaaaccgcggttcttcttcctaattc-----gagcctc--c Cat -cccctaagaa-ccccgg---ttcttcctaattc-----gggcctc--c Cow ------------------ctcctcttcctagtcg-----cagcctc--c Platypus -cgggcagggaatgtatctgtttattgctgtatt----gtactctc--c Opossum ================================================= Chicken ================================================= X. tropicalis ================================================= Alignment block 19 of 66 in window, 80055958 - 80056446, 489 bps B D Rat agcat----------c-caaagatttcc----tagattgggagaaa--tcttcaaagcaaatctgatcca B D Mouse agcat------------caaagatttcc----tagactgggagaaa--tcttcaaagcaaatctggtcca Prairie vole aggat-------------agatataccc----tagattaggaaaaag-tgttcaaagcaaatctggttca B D Guinea pig ggcat---------gt-aggataaatcc----tagactcgggaaaggttcctccaagcccgtctgatcaa B D Rabbit ggcat------------gggagacttcc----aggatc-----aaagtctctccaagcccacccggttta B D Human agcatcggagacttct-aggataaatcc----aaggctcaggaaaagtccttccaagaccatccggtcca B D Chimp agcatcggagacttct-aggataaatcc----aaggctcaggaaaagtcctcccaagaccatccggtcca B D Rhesus agcatcggagacttct-aggataaatcc----aaggctcagaaaaagtccttccaagaccatccggtcca B D Tarsier aacatccgagacttga-aggataaatct----tagattcttgaaaagtccctccgagcccatccagtcca B D Dog agcatcggaggtttcc-agaagaaatcc----taggctaagg-aaagtccctctaaacccaccaggtcca B D Panda agcatcggaggtttccaaggataaatcc----tagactcgggaaaaggccctctaagcctatcaggttca B D Cat agcatcggaggtttcc-aggataaatcctagatagactcagaaaaggtccctctaaaatcatccggtccc B D Cow agcatcagaggtttct-a-------------------------gaagtccctccaaacccatcctgccca B D Opossum ====================================================================== B D Chicken ====================================================================== B D X. tropicalis ====================================================================== Rat -----------------gccta--ctgcagtcct----gac-gaagaaattgcaaacgggtgatggaga- Mouse -----------------gccta--ccgcagtcct----aac-gaggaaattgcaatcgggtgatggaaa- Prairie vole -----------------tctta--ctgcagttct----gac-gggaaaaacgaaaaccg--ggtggaga- Guinea pig -----------------atata--ccgcaaacctgatggac-agacaaatcaaagctcggtaggaggaa- Rabbit -----------------gcctacccctcgatact----gac-gtggaaaccgaagcccagcgaggggaa- Human -----------------gccta--cctcaaactt----gat-ggggaaatcgaggcccagtgagagagag Chimp -----------------gccta--cctcaaactt----gat-ggggaaatcgaggcccagtgagagagag Rhesus -----------------gccta--cctcaaactt----gat-ggggaaatcgaggcccagtgagagagag Tarsier -----------------gccta--ccacaacctt----gat-ggcgacatcaaggcccagggagagaaag Dog -----------------gccca--cctcaatcct----gat-ggggaaatcgaggccgagagagaggaa- Panda -----------------gccca--ccccaatcct----aac-ggaaaaatcaaggccgagagagaggaa- Cat tctaaatccatcagattgccca--ccccaatcct----gat-tgggaaatcgaggccgagagaggggaa- Cow -----------------gccca--cggcaatcct----gatgggggaagtctaggcccagcgagaag--- Opossum ====================================================================== Chicken ====================================================================== X. tropicalis ====================================================================== Rat --------------------cttctaaataaatggttt--gggcacagagctcagatctacc-ag-tgtt Mouse --------------------tttctaaatagatggctt--gggcatagaactcagttctacc-ag-tgtt Prairie vole ------------------ctcttctaaatagatggcttg-gggcgtagaactcagatctacc-ag-tgtt Guinea pig --------------tgggttcttccaaataatttacttg-aagtgtggaacccagacctccc-aa-gctc Rabbit --------------gggaggcttccaag-agttgcctttcgggcgtggaacccaaaaccctc-ag-cctg Human gggagatggaggaagggactcttccaaatagttgactaa-aggcgtagaaccctgaaccccc-ccgtctt Chimp gggagatggaggaagggactcttccaaatagttgactaa-aggcgtagaaccctgaaccccc-ccgtctt Rhesus gggagatggaggaagggactcttccaaatagttgactaa-aggcgtagaaccctgaaccccc-tcgtctt Tarsier gagagagagaggaagggacccttccacatagttgactta-aggcttagaaccctccactccc-at-cctt Dog --------------gggactcttccaaatagctgacttt-cagattggaacccagaattccc-ag-tgtt Panda ---------------gcactattccaaagag----cttt-ctgattggaacccagaactcccaag-tctt Cat --------------aggactcttccaaatggctgacttt-cagattggaacccagaactccc-ag-tctt Cow ---------------ggactcttccaaatatctgacttt-aggattagaacccagaactcca-ag-tctt Opossum ====================================================================== Chicken ====================================================================== X. tropicalis ====================================================================== Rat tctat------gcggatgcatcctcttcagaggggtcta--atcataaaacaagcctgaaaccttatttt Mouse gctat------gaggactcgtcatcttcagtggggtct---atcacaaaacaagcctgaagccttatttt Prairie vole gctat------actgacccttcatattcagaaagtgct---attacaaaacaagcctgaagccttagtct Guinea pig actacagcgcagcagacccttcctcttaagggggagctgctattacaagaggagc--gaagccttc---- Rabbit acgac-----tccggagcctttctttccagggggcgcg-------------------------------- Human actat-----ttcagacctttcctcttaaaaggaagctactgttgcagaaccagcccgaagccttattcc Chimp actat-----ttcagacctttcctcttaaaaggaagctactgttgcagaaccagcccgaagccttattcc Rhesus actat-----ttcagacctttcctcataaaaggaagctactgttgtaaaaccagcccgaagccttattcc Tarsier cctgc-----tccagacccttgctcctaagggggcgcgac--ttacagaacaagcccgaagccttattcc Dog actac-----tgcagactctccctcttaggtagaaccacctattacagaacaagcccaaagcctcagttc Panda actac-----tccagacccttcctcttagggagaaccacctattgcagaacaagtccgaagcctcagttc Cat actac----ttccagactcttcctctgagggagaaccacctattacagaacaagcccga----------- Cow actac-----tccagact----ctcttacggggtaaccgctattacaaaacaagcccgaagcctcattgc Opossum ====================================================================== Chicken ====================================================================== X. tropicalis ====================================================================== Rat gttgggaa-ggggcatacgctcaagtgatggataaagaaatagcacaggcggcaagggctaaacgataa- Mouse gttgggta-ggggcacgcgctcaagtcatggat----aaatggcacaggcggcaaaagccaaatgataa- Prairie vole gttggaaa-gggacatgggttcaaatgatggaaaaagagatggcaccagaggcaagggcc-----atac- Guinea pig -ttgggtacggagtatgcgctctaatgacagcgaaagaa--ggcacctgcggctagggccagtggatac- Rabbit -ttgggag-ggggcttgcgctccggggaggcagc---cggtggcacctgcggccagggcc-ccaggtag- Human tttggtaa-gggtcatgcgctcagatgacgaaga---cggtggcatctgcggttagggccgtacgctaa- Chimp tttggtaa-gggtcatgcgctcagatgacgaaga---cggtggcatctgcggttagggccgtacgctaa- Rhesus tttggtaa-gggtcatgcgctcagatgacgaaga---ctgtggcatctgcggttagggccgtacgctaa- Tarsier ------aa-ggggcgcgctctcaaatgacgggga---cggtggcacctgcggccagggccatacgataa- Dog gttagcaa-cgggcatgcgctctatcgacggaga---ccgcagcacctgcagcttgggccagacgacac- Panda gttagcac-cgggcatgcgctctaacgacggaga---ccgcagcacctgcggctagggccgtacgatac- Cat --tagcaa-cgggcatgcgctctattgacggaga---ccgcagcacctgcggctaccgccgtacgatac- Cow gttggaaa-ggggtatgcgctctaagaacggaga---cggcggcacc-gcagctagggccatatggtaca Opossum ====================================================================== Chicken ====================================================================== X. tropicalis ====================================================================== Rat -----ggccacgctaacc------------------cgagactc--aatatgaagggaaagagggaaatg Mouse -----gaccacggtaacc------------------tgagactc--aatacgaagggaaagagggaaatg Prairie vole -----aaccacgttaacg------------------tgaaagtc--tatacgaaaggaaatgaaggaacg Guinea pig -----agccacgtcaacc------------------tgggactc--ta---gaagggaaagtgggaaatg Rabbit -----cgccacgtcaaac------------------cgaaactc--gg---aaagaggaagcggggagag Human -----agccacgtcaacc------------------ctg-------gg---taacagcggggagggaatg Chimp -----agccacgtcaacc------------------ctg-------gg---taacagcggggagggaatg Rhesus -----agccaagtcaacc------------------ctg-------gg---taacagcggggagggaatg Tarsier -----agccacgctaacc------------------ctagactt--gg---gaagaggaggcagggaatg Dog -----agccacgtcaacc------------------tgagacctcagg---gaaggggaggcggggaatg Panda -----agccacgtcaacc------------------tgagacctcggg---gaaggggaggcggggaatg Cat -----agacacgtccacc------------------tgagacctcacg---gaagcgcaggcgggg--tt Cow gacaaagccaggtcaacccaacctagggtcttcccgtgagaccttggg---gaaggggaggcaaggagta Opossum ====================================================================== Chicken ====================================================================== X. tropicalis ====================================================================== Rat ac----------gctggctgggccccagccaaggcttacccgcagatcccggctccgtgatacctcctca Mouse ac----------gctggctgggcaccagccagggctcacccgcagatcccggctccgtgacatctcctca Prairie vole ac----------ggtgtccgggtcccagccagacctcacccgcagatctcggttccgtgacagctcctga Guinea pig acggt-ccctagggtgcccggagccccactgggcctcacccggaactcacgaccccttgacagctcctcc Rabbit agggc-cctcc-agtgcccgcgccgc-gcccagcctcacccgc---------------ggcagctcctcg Human agggt-ccccgcggtgcccgggtccccgcccagcctcacccgcagctcccggcccagcggcagctcctca Chimp agggt-ccccgcggtgcccgggtccccgcccagcctcacccgcagctcccggcccagcggcagctcctca Rhesus agggt-ccccgcggtgcccgggtccccgcccagcctcacccgcagctcccggcccagcggcagctcctca Tarsier aggacgccccgcggtccccgggtccccgcccggcctcacccgcagctcccggccctgcggcggctcctca Dog agggc-tcccgcggtgcccgtgcccctgccgggcctcacccgcagctcccggccccgcggcagctcctca Panda agggc-tcccgcggtgtccgtgcccctgcccagcctcacccgcagctcccggccccgcggcagctcctca Cat aagg--------ggtacccgtgtccctgcccagcctcacccgtagctcccggccccgcggcagctcctca Cow aaggg-ttccgcagtgcccgtgtccccgcctgtcctcacccgcagctcccgccccagcggtagctcttca Opossum ====================================================================== Chicken ====================================================================== X. tropicalis ====================================================================== Rat accccagggtgccagctattccagacgatataaaaagccaagcccagggccagcgccagcagcagcaggg Mouse accccagggtgccagctgttccagacgatatagaaagccaagcccatagccagcgccagcagcagcaggg Prairie vole accccagggtgccaggcgttccagacgatgtagaaagccaagcccagggccagagcaaacagcagcagag Guinea pig gtcccgcggtgccagccgctccagataatgtagagcgcgaagcccacggccacggc---cagcagcaggg Rabbit gtcctgcggtgccagctgccccacagcgtgtagagggccgagcccacggccagcgccagcagcagcacgg Human gtcctgcggtgccagccgctccaaatggtgtagaacgccgagcccacggccagcgc---cagcaacagag Chimp gtcctgcggtgccagccgctccaaatggtgtagaacgccgagcccacggccagcgc---cagcaacagag Rhesus gtcctgcggtgccagccgctccaaatggtgtagaacgccgagcccacggccagcgc---cagcaacaggg Tarsier atcccgcggtgccagccgctccaaatggtgtagaacgccgagcccagggccagcgccagcagcagcaggg Dog gtctggtggtgccagccgctccagatggtgtaggtcgccgaagccagggccagggccagcagaagcagag Panda gtctggcggtgccagccgctccagatggtgtagaacgccgaggccacggccagggacagcagaagcaggg Cat gtctggcggtgccagccgctccagatggtgtagaacgccgaggccacggccagggacagcagaagcagag Cow gtctggctatgccagatcctccaaatggtatagaacaccgaggctaccgtcagagccagcagcagctggg Opossum ====================================================================== Chicken ====================================================================== X. tropicalis ====================================================================== Rat gcaggagctgcacccgcggcagaagacggcgcttggaaag Mouse gcaggaactgcactcgcggcagaagacggcgcttggaaag Prairie vole gcaggagccgcactcgcggtatcaggcggcgcttggaaag Guinea pig gcaacggctgcacccgcggtagcaggcggcgcttgggcag Rabbit gcagcagctgcgcccgcgggagcaggcggcgcttgagcgg Human gcaagagccgaacccgcggtagcaggcggcgcttcggcgg Chimp gcaagagccgaacccgcggtagcaggcggcgcttcggcgg Rhesus gcaagagccgaacccgcggtagcaggcggcgcttcggggg Tarsier gcaagggctgcacccgcgggagcaggcggcgcttcggctg Dog gcaagaagtgcgcccgcgggagcaggcggcgcttgggcgg Panda gcaagaagtgcgcccgcggtagcaggcggcgcttgggcgg Cat gcaagaagtgcgcccgcggtagcaggcggcgcttgggcgg Cow gcaacagctgtgcccgcggtatcaggcggcgcttgggcgg Opossum ======================================== Chicken ======================================== X. tropicalis ======================================== Alignment block 20 of 66 in window, 80056447 - 80056523, 77 bps B D Rat tgagggtggtttcatgaggccgcgatccccgagccgctgccgagaccgcccgcggctggccggactcatg B D Mouse tgagggtggtttcatgaggccacgatcctcgagccgctgccggggccgcccgcggctcccgggactcatg Prairie vole agagggtggctgcatgaggccccgatccccgggtcgctgtcggggccgcccgcggctcccgagactcatg B D Guinea pig tgagggtgactctaggagcccgcgttcgccgagccgctgccggggccgcccgcggcccccggatcgcatg B D Rabbit cgagctcggctccatcaggccgcgctccccgagccggggccggggccgcccgcggcccccgggacgcatg B D Human caagagtggctccatgaggccacgttcccccagccgcaggcggggtcgcccgcggcccccggaacgcatg B D Chimp caagagtggttccatgaggccacgttcccccagccgcaggcggggccgcccgcggcccccggaacgcatg B D Rhesus caagagtggctccataacgccacgttcccctagccgcaggcggggccgcccgcggcccccggaacgcatg B D Tarsier cgagggtggctccgagaggccacgctccccgagccgcagccggggccgcccgcggcccccggaacgcatg B D Dog ggagggcggctccaagaggccacgttccccgagccgtagccgggaccgcccgcggcccccggaaggcatg B D Panda tgagggtggctctaagaggccacgttccccgagccgtagccgggaccgcccgcggcccccggaaggcatg B D Cat tgagggtggctccaagaggccacgttcccccagccgtagccggggccgcccgcggcccccggaaggcatg B D Cow tgagggtcgctccaaaaggctgcgttccccgacctggagccggggccgcccgcggcccccggaaggcatg B D Opossum tggggttggctt-----ggcagtg----ccgaggggtcaccgaagccgcctgggcctggccgggcaaacg B D Chicken ====================================================================== B D X. tropicalis ====================================================================== Rat gcagctt Mouse gtagctt Prairie vole gcagctg Guinea pig gcagc-- Rabbit gcagctt Human gccgctt Chimp gctgctt Rhesus gcagcta Tarsier gcagctt Dog gcagctt Panda gcagctt Cat gcagctt Cow gcagctt Opossum cgggctt Chicken ======= X. tropicalis ======= Inserts between block 20 and 21 in window B D Opossum 5993bp Alignment block 21 of 66 in window, 80056524 - 80056915, 392 bps B D Rat tgccctgaaaccaatccccccgcagggtggtttgag-tttag-----gccaagattcgcctctcggaggt B D Mouse tgctctgaaaccaat--cccggtatggtggtttgagttttag-----gccaagatccgcctcgctgaggt Prairie vole tgccctgaaaccaat--ccacggactgtagtttgag-tttag-----gccaagatccgccccttgtgaat B D Guinea pig tgtcctgaaacgtgt--acccg-gccgcagaaggag-tttaggccccgccaagttccaccca--aggaat B D Rabbit tgccctgaaaccgg---ccagggaccgcggatggag-ttcaggcccagccaagtccca-ctctatggaat B D Human tgccctgaaacctgt--accag-accacggattgag-tttaggcccagccaagttcct-ccccatggaat B D Chimp tgccctgaaacctgt--accag-accacggattgag-tttaggcccagccaagttcca-ccccatggaac B D Rhesus tgccctgaaacctgt--accag-accac-gattgag-tttaggcccagccaagttcca-ccccatggaat B D Tarsier tgccctgaaaccggt--cccgg-accgcagactgag-tttaggcccagccaagttcca-ccctcgggaat B D Dog cgccccgaaaccggt--cccgg-accgcggat--ag-tttaggcccagccaaatccca-ccccatggaat B D Panda cgcccagaaaccggt--cccgg-accgcggat--ag-tttaggcccagccaaatccca-ccccatggaat B D Cat cgccctgaaaccggt--ccggg-accgcggat--ag-tttaggcccagccaaatccca-ccccatggaat B D Cow ggccctgaaacgggt--cggag-acggcggatagag-ttaaggcccagccaagtcccg-ccccatgaaat B D Opossum ====================================================================== B D Chicken ====================================================================== B D X. tropicalis ====================================================================== Rat ta-caaatgccaataaagaaacacagtaac-tgcgtcctccc----------------------ccaat- Mouse ta-caaaacccaataaagaagcagagtaac-tgcgtccttcc----------------------ctgaga Prairie vole ta-caaaagccaataaaaaaggagagtgcc-tgcgtcgtccc----------------------gccaga Guinea pig ca-caaaa-ccaatgagcaacaagagcggc-tgcacgtccca----------------------cccag- Rabbit ca-caaag-ccaatgagcgacaagagcgccgggcaccactcc--------------------ggctcgg- Human cg-gtggg-ccaataagcaacagctgcggc-tgcaccagcccaccccacagcgagcagcgaaaccaata- Chimp cg-gtggg-ccaataagcaacagctgcggc-tgcaccagccc------------------accccacag- Rhesus ca-gtggg-ccaataagcaacagcagcggc-tgcacctgccc------------------accccacag- Tarsier ca-accga-ccaatgagcagccaccgcggc-tgcaccatcccac----------------cccccccag- Dog ca-ccgaa-ccaataaacacgaagagcggc-tgcaccatccc------------------acccaccct- Panda ca-ccgga-ccaatgaacaagaacagcggc-ggcaccatccc------------------accctccct- Cat ca-ccgga-ccaatgaacaagaagagcgac-tacaccatccc------------------accctttct- Cow aagccgga-ccaatgagcaacaagagcggc-tgcaccat-cc------------------gccctcccg- Opossum ====================================================================== Chicken ====================================================================== X. tropicalis ====================================================================== Rat cga------------------------------------------------------------------- Mouse cga------------------------------------------------------------------- Prairie vole tga------------------------------------------------------------------- Guinea pig tgagc------------------cct-------------g------aaaccaatggcatcctgaggacac Rabbit cgagctggg-------tgcagctctc-------------g------aggacaagcctccccggaggcccg Human agaactacggtcct-------------------------g------aggacacgcctcccagcctccctt Chimp cgagcagcgaaaccaataagaactac-ggtcct------g------aggacacgcctcccagcctccctt Rhesus cgagcagcgaaaccaataagagctac-------ggtcctg------aggacacgcctcccggcctccctt Tarsier cgagcggcgaagccaatgggcactgt-------------ggtcctgagccccagcctccccgcctccctg Dog cggtcagtgaaaccaatggcgaccctcactctg-------------agaacacgccttcctgtctccctg Panda cggtcagtgaagccaatggggactctcgttctg-------------agaacacgccttcttgtctccctg Cat ctacgggtgaagccaatgcggactctcgttctg-------------agagcacgccttcctgtctcccta Cow cgagcagtaaagccaatg-ggactttcggcctg-------------aggactgggctcctttccttcagg Opossum ====================================================================== Chicken ====================================================================== X. tropicalis ====================================================================== Rat -----------------------ttgcgattggct-ctcctaagcgccgcaccaccc-aaaagggagcgc Mouse -----------------------ttgcgattggct-gtcctaagcgccgccccaccc-aaaaaggagggc Prairie vole -----------------------ttgcgattggtt-ggactaaacgtcgtacaaatc-aaaagacagcgc Guinea pig gcc-tgcctaccgccagtgggtgttggcgttggtt-tccctttgggttgcacaaccc-gaaagagcgcga Rabbit ggg-tg-----------------tcgcgattggct-cccagagggtttgcacaagac-cagaggggacgc Human agg-ta-----------------ttggggttggtt-cccctgagaatggcacgaccc-aaatgggagcgc Chimp agg-ta-----------------ttggggttggtt-cccctgagaatggcacgaccc-aaatgggagcgc Rhesus ggg-ta-----------------ttggggttggtt-cttctgagaatggcacgaccc-aaaagggagcgc Tarsier ggg-tg-----------------ttggggttggttccccctgagtattgcacaaccc-aaa-gggagcgc Dog ggg-ct-----------------ttggggttggtt-cccctgagggttgcacaacccaaaagggtagtgc Panda gggttt-----------------ttggggttggtt-cccctgagggttgcacaaccccaaaagggagcgc Cat ggg-ct-----------------ttgggggttggt-cccctgagggttgcacaaccc-aaaagggagcgc Cow gagctt-----------------tgggggttggtt-ccccc--gggttgcacaaccc-caaagggagagc Opossum ====================================================================== Chicken ====================================================================== X. tropicalis ====================================================================== Rat ggaaaccttaaggcccgcccccacgggagagaaacaggcaatgagctgtgtccgaatatacgaaac---- Mouse ggaaaccttaaggcccgcctccacggaagaggaccagtcaatgggctgcgtccgaatgtgcgaaac---- Prairie vole ggaaaccatggggcccgcc-ccatgaaagagaaacagccaatgagttgcctctgactgt----------- Guinea pig gaaaggggtagggaccgcctcca---aggggagtgggccaatgggcagcatttgatcat-agagacgcac Rabbit g-aaggcgtgcgacccgccccagcggagcgggtagatgcaatgggcagcgaccggtcgc-ggaaag---- Human aagagaagtaggctccgccttagcggaggagggaaagccaatgaacagcgtttgatcat-ggaaaatatt Chimp aagagaagtaggctccgccttagcggaggagggaaagccaatgagcagcgtttgatcat-ggaaaatatt Rhesus aaaagagataggctccgccttagcggagg-gggaaagccaatgaccagcgtttgatcgt-ggaaaatatt Tarsier ggaaggggcaggctccgccttagcggaggagggaaagccaatgagcagcgtctggtcgt-ggaaaatatt Dog gaaagggagaggctccgcctcaacggaggaacggaagccaatgagcaatgtttgatcct-gaaaaacgtt Panda gaaatgggtaggctccgccttagcggaggaaaggaagccaatgaaaaatgtttgatcgt-ggaaaacatt Cat gaaaggcataggctccacctcagcggaagaagggaaaccaatgagaaatgtttgatcat-ggaaaacatt Cow gtaagaagtaggcgccgccccagcgcaggaggggaagccaatgagaagcgtttgatcac-cgaaaacatt Opossum ====================================================================== Chicken ====================================================================== X. tropicalis ====================================================================== Rat ---cttccccggcgcggggccacgccccttacggaagtcga----------------------------- Mouse ---cttccaaggcgcggggtcacgcccctcacggaagtcga----------------------------- Prairie vole -----------gcgtgaagccacgccccttac-tatgtcac----------------------------- Guinea pig gcacctcccctgcccaggtccaggtcccttacagatgtagaattgttcttcccagatt-----tgaa--- Rabbit ----------ggattggttccgcg---------------gg----------------------------- Human cgatctcccgggcgcaggtccatgccccttccggatgtagg--------caggggattggtggcgca--- Chimp cgatctcccgggcgcaggtccatgccccttccggatgtagg--------caggggattggtggcgca--- Rhesus caatctctcgggcgcaggtccatgcccctcccggatgtagg--------caggggattggtggcgca--- Tarsier cgatcacccgggcgcaggtccacgcctctcccggacgtagg--------taagggattggttgttaaggt Dog ggac---caaggagcaggtctccgcccctcccgtaggaagg--------caaaggattggttactcg--- Panda ggac---ccaggcgcaggtccacgcccctcccgtatgaagg--------cgaaggattggttactcg--- Cat cgac---ctaggcgcaggtccacgcccctcgtgtatgaagg--------caaaggattggttactcg--- Cow agtcttactgggcgcaaatccacgccgctcccggatggacc--------c----------tctccct--- Opossum ====================================================================== Chicken ====================================================================== X. tropicalis ====================================================================== Rat ----------------------------tcaagaaactgtggttcaagg-aaaaaggggcggcatccat- Mouse ----------------------------tcaagaaactgtcgttcaaggaaaaaaggggcggcatccat- Prairie vole ----------------------------tcaagaaac---acatcaagg-aa-------------ctgt- Guinea pig ----agat---------caatggtcacctcagggagccatgcctgaagg-aa-aaagggtagtgcgcat- Rabbit ----------------------------acgagaaga------tccagc-ga--------ggcgtcagtg Human ----gggtcggaaagatcagtagatacgtcagtaacgcgtcccagaggg-aa-gaggggcggtgcctgt- Chimp ----gggtcggaaagatcagtagatacgtcagtaacgcgtcccagaggg-aa-gaggggcggtgcctgt- Rhesus ----gggtcggaaagatcagtagatacgtcaataacccgtcccagaggg-aa-gaggggcggtgcctgt- Tarsier aagggggtcggaacgatcaatagacacgtcaataaaccgccccagaggg-aa-agggggcggtgcccat- Dog ----aagtcggaaagatcaatagacacgtaaacgaaccgacaccgatgg-aa-aaggggcggtgcccgt- Panda ----gagtcggaaagttcaatagacacgtaatagaaccgaccctgaagg-aa-aaggggcggtgtccgt- Cat ----gagtcggaaagctcaatagacccg-aaaaggaccgtccctaatgg-aa-aaggggcggtgtccat- Cow ----ggtccagaaaatccaatatacacgtaaatcaacagttcccgaagg-aa-agggggaggtgcccat- Opossum ====================================================================== Chicken ====================================================================== X. tropicalis ====================================================================== Rat ccctaaaacaaggaaccgattggtttgc-ctgaagccatgccctcaaga-aaattgtcggcgggtatttt Mouse ccctaaaacaaggagccgattggtttac-ctgaagccatgccctcaaga-aaagtgtccgagggta-ttt Prairie vole ggctcaatcagggagtcgattggttctc-cagagaccacgcccccaaggccaagagtcggcgggtg-ttt Guinea pig ccctaaagctaagagcggattggcttcg-ccgaggccgcacccccaaag-ataggaccggcttgtc---- Rabbit ccccgaagccgggaccggattggcttcg-tggaggccgcgcccccggag-acggggccggcgggca-ttt Human ctccgaagcgaggagcggattggcttca-cggaggccgcgcccccgaag-tcacggccggcgggca-ttt Chimp ctccgaagcgaggagcggattggcttca-cggaggccgcgcccccgaag-tcacggccggcgggca-ttt Rhesus ctccgaagcgaggagcggattggcttcagcggaggccgcgcccccgaag-tcacggccggcgggca-ttt Tarsier ccctgaagcgaggagtggattggcttag-cggaggccgcgcccccgaac-tccgggtcggcgggca-ttt Dog cccagaagcgaggagccgattggctaca-cggaggccgcgcccccgagg-gcggagccggcgggct-ttt Panda ccccgaagcaaggaaccgattggcttcc-cggagaccgcgcccccaaag-gcagggacggcgggca-ttt Cat ccctgaagcgaggagccgattggcttcg-cggaggccgcgcccccggag-gcagggccggcgggca-ttt Cow ccctgaagcgaggagcggattggcttct-cgaaggccgcgcccccaaag-gcagagctggagggca-ttt Opossum ====================================================================== Chicken ====================================================================== X. tropicalis ====================================================================== Rat ggaaaccgggttgcgttttcctt Mouse ggaaatggggttgtgttttccat Prairie vole ggaaacggcgctgcgtgccccgt Guinea pig --------------gcctccctc Rabbit agaaacctctggccgtttccctc Human ggaaatagcttgtcatttccctc Chimp ggaaatagcttgtcatttccctc Rhesus ggaaatagtttgtcatttccctc Tarsier ggaaatgaagtgtcgttttcttc Dog gg-aatgccgtgtcctgtccctt Panda gg-aatggggtgtcctttccctc Cat gg-aatggcgtgtcctttccctc Cow gg-aaatggctagtatttccctc Opossum ======================= Chicken ======================= X. tropicalis ======================= Inserts between block 21 and 22 in window B D Cow 414bp Alignment block 22 of 66 in window, 80056916 - 80057045, 130 bps B D Rat ctcccaactagacagtta-ggcgggaaaacaatttcagtcagaccccgttttattttccgc--------- B D Mouse cttccaactggacggttt-gacgggaaaataattctagtcagaccccgtattattttcctc--------- Prairie vole cctc---ctagactgtcg-gacagggagctaactcgactcaggcccccctttatttccctctcctagtct B D Guinea pig cttcaatttacacttttt-tacaacaaaaccactcgagtcgtgccccctttattttttctc-tccattgt B D Rabbit ctgcagcctgtcccgcctctaccacgaagcggcgcgactcggactctctgtc-ttggtctc-tccatccc B D Human cttcaacctgtaccattc-ttcaa-gaaacggtttgaatcagactgcctttc-cttttgtc-ttcattgt B D Chimp cttcaacctgtaccattc-ttcaa-gaaacggtttgaatcagaccgcctttc-cttttgtc-ttcattgt B D Rhesus cttcaacctgtaccattc-ttaaacgaaacggtttgaatcagaccgcctttc-cttttgtc-ttcattgt B D Tarsier ctttaacctctaccgttc-cacagcaaaataatttgaatcagaccccctttc-tttcta---ttcattgt B D Dog cttcagcttgtgccgctc-tacaacgaaacgatttgagtcggacccgcttta-ttcttctc-tccattgt B D Panda cttcaacctgtgccgttc-tgcaacggagtgatttgagtcgaatccgttttc-ttcttctc-tccattgt B D Cat cttcagcctgtgccactc-tacgacgaagtgatttgagtcggccccgt-----ttcttctc-tccattct B D Cow ====================================================================== B D Opossum ====================================================================== B D Chicken ====================================================================== B D X. tropicalis ====================================================================== Rat -atgagcagacaa-cctattgtgatcctcagaggcttcaaat--cctccctataggcattttctgcagga Mouse -atgagcagacac-cctattgtgatcctcagaagcttcaaat--cctccttataggcattttctacagga Prairie vole tgagcgcagac-c-cctactgtgctcctcaatggcctcggat--cctc----taggcattttctaaggcg Guinea pig tgtgagcatct-g-tcttgtgttgtcctaagtggcttcgaa---ccacaaaatcagagttttacccaact Rabbit gatgaacacct-g-cccgctgtggtccttaatggcctcgaac--tgccgctcgcggcttcggccccctcg Human cataaacatct-gcccccgtgtggttctgactggccgcgaac--ccctacccgaagcttttattccatca Chimp cataaacatct-gcccccgtgtggttctgactggcctcgaac--ccctacccgaggcttttattccatca Rhesus cataaacatct-g-ccccgtgtggttctgactggcctcgaac--ccctatccgaggcttttattctttca Tarsier cgtgagcacct-g-cctcatagggtcccgaatggcctcgaaccacactgctccaggcttttatcccatcc Dog c-------ttc-t-ctccatatggtcctgaaagaccctgagc--tactacgcagtgcttctaccccacgt Panda cgtgaatatct-a-tcccgtatggtcctgaaagaccttgaac--tactacgcgatgcttctaccccacct Cat cgtgaatatct-g-ccccgtacggtcctaaaagacctggaac--cactacgcgaggcttctactccacct Cow ====================================================================== Opossum ====================================================================== Chicken ====================================================================== X. tropicalis ====================================================================== Rat gagc Mouse gagt Prairie vole gcgc Guinea pig ccgt Rabbit ctgc Human ttgt Chimp ttgt Rhesus ttgt Tarsier ttag Dog ctgc Panda ccgc Cat ccgc Cow ==== Opossum ==== Chicken ==== X. tropicalis ==== Alignment block 23 of 66 in window, 80057046 - 80057413, 368 bps B D Rat gta--gcc-------tt--agagtcactatggtaacagggcacgcccac-agtcg--------tgattgc B D Mouse gca--gcc-------tg-aagggtcgctatggtaacaggccacgcccac-agccgctggtatttggttgc Prairie vole gca--aca-------aa--ttgatcattatgaagacagggcacgcctat-ctccgctgaggt-ggattgc B D Guinea pig gca--gct-------gg-tgtggtagctatggcaacaggccacacccat-tat-gctgtttg-ggtttgc B D Rabbit gca--gcc-------ggcgggggtcgctatggcaacaagccacgcccca-gcccgccgggtg-ggtttgc B D Human gcaccgtt-------ggtggggaatgctgtggcaacaggccacgcctcc-acttactggttg-gctttgc B D Chimp gcaccgtt-------ggtggggaatgctatggcaacaggccacgcctcc-acttactggttg-gctttgc B D Rhesus gcaccgtt-------ggtgggcaatgctatggcaacaggccacgcctcc-acttactggttg-gctttgc B D Tarsier gcacggct-------ggcggggatcgctatggcaactggccacgccccc-gctcgctgtttg-ggtttgc B D Dog gcggggcc-------ggcgcggattgccacggcaacaggcctcgcccacaccgtgcaggttg-ggattgc B D Panda gcggggct-------gacgcggatcgctatggcaacaggccacgccccc-----gcaagtta-ggattgc B D Cat gcaggcct-------ggcgcggatcgctatggcaacaggccacgccccc----ccctggttg-ggattgc B D Cow gtagcctccgccgaaggcggaggtcgctatagcaacgggccacgcccca--ctcgctggcta-ggtttgc B D Opossum ====================================================================== B D Chicken ====================================================================== B D X. tropicalis ====================================================================== Rat gcaggcgtcgacggaagtcagccgcaggagacggaagtcccgcccttctcttgctgtg-ctc-caaaggc Mouse gcaggcgccgacggaagtgagccgcaggagacggaagtcccgcccttctcgccctgta-cgc-caaaggc Prairie vole gcaggcgccgacggaagtgagccgcaggaggcggaagtccctccctcctctcgctcta-ctc-cggggac Guinea pig gcaggcgctaacggaagtgagacaacggaaacggaagtccctcccctcttcttc-----ctt-ctgagac Rabbit gcaggcgcccacggaagtggcccgccggaagcggaagtcccgcccctctcgcgctccatccg-cagaggc Human gcaggcgccaacggaagtgggtcgcaggaagaggaagtcccgcctctct----------ctc-ctcaggc Chimp gcaggcgccaacggaagtgggtcgcaggaagaggaagtcccgcctctct----------ctc-ctcaggc Rhesus gcaggcgccaacggaagtgggtcgcaggaagaggaagtcccgcctctct----------cgc-ctcaggc Tarsier gcaggcgtgggcggaagtgggccgcaggaagaggaagtcccgcctctct----------cct-cagaggc Dog gcaggcgccgacggaagtcggccacaggaaacggaagtcccgcctgtagccctct----ctt-cagaggc Panda gcaggcgcggacggaagtgggccgcaggaaacggaagtcccgcctctcgctctct----ctt-cagaggc Cat gcaggcgccaacggaagtggaccaagggaaacggaagtcccttctgtagctctag----ctt-cagaggc Cow gcaggcgcgcgcggaagtgggccgtaggaagaggaagtcccgcctctggctctct----gttccggaggc Opossum ====================================================================== Chicken ====================================================================== X. tropicalis ====================================================================== Rat taaagcaacgcgcttggag------gcgggagtgatctgctagcgaaacctt---caccatgtgaggccg Mouse tggagcaacgcgcttggag------gcgggagtgatctgcgagcgaaaccta---caccatgtgaggccg Prairie vole ctgagcaacgcgc-tgccg------gcgggagtgatctgcaagcaaaacctc---caccatgtgaggccg Guinea pig cgaagcaacgcaa-aggga------agaagagtaacccgaggtcgcggctgc---caccatgtgagactg Rabbit agaagcaacgcgg-aggaggttggagtgagagtgacccgaacgcggggccgg---caccatgtgaggccg Human agcagcaacgcgg-aggaa------acgggagtgaacggagagcgtagtgac---catcatgtgaggccg Chimp agcagcaacgcgg-aggaa------acgggagtgaacggagagcgtagtgac---catcatgtgaggccg Rhesus tgcagcaacgcgg-aggaa------acgggagtgaacggagagcttagtgac---catcatgtgaggccg Tarsier tgaagcaacgcgg-agaag------acgcgagtgacctgagagcgcagccgc---cagcatgtgaggccg Dog aggagcaacgcgg-ggaag------acggagctgatctgcgagcgcagccgctaccaccatgtgaggcc- Panda agcagcaacgcgg-aggag------acggcgctgacttgggaccgcagccacttccaccatgtgaggccg Cat gggagcaacgcgg-acgag------acggcgctgaactgagagcgcagccgctaccaccatgtgaggccg Cow a----caccacgg-aggag------acggtagtgacttgaaaacgcggtcaccatcatcatgtgaggccg Opossum ====================================================================== Chicken ====================================================================== X. tropicalis ====================================================================== Rat ggacgggcttcggcgg-ggacacgaagatggagggggacgg-tttagctaaataacaatcgaaatggggt Mouse ggctgggctttggcgg-ggccgtggagatggaggtggacag-tttagctgaataacggtcgaaatggggt Prairie vole ggcggggcttcggcag-ggtctggaaggtggaaggggacag-tttagcagattaacggttgaagaggggt Guinea pig ggctggttttcaaccg-caggagggagttgagggtgta-aa-tttggctgcttaactgtgggag-aggat Rabbit ggctgggcttaagcggcgggcgtgaggttgtgggtgcg-aa-tgcggccgattagcggcggaag-ggggc Human ggctaggcttaggcggcgggaatgaggttgagggtgga-ta-tttgaccgattgagtgtgggaa-gggtt Chimp ggctaggcttaggcggcgggaatgaggttgagggtgga-ta-tttgaccgattgagtgtgggaa-gggtt Rhesus ggctaggcttaggcggcgggaaggaggttgagggtgga-aattttgaccgattgagggtgggaa-gggtt Tarsier gcctaggcttgggcggtgggagtgaggttgagggtgta-aa-tttgggcgattaccggtggaag-gggat Dog -------------cggcgggagtggggtcgagggcgta-ga-tgtggccgtttgccggt--------ggt Panda ggctgaattttggcggcgggagtggggttaagggcgta-aa-tgtggtcgcttaccggt--------ggt Cat ggctaggctttggcggcgggagtggggttgagggcgta-aa-tgtggccgcttatcagt--------gat Cow ggctgggtttgggtggcgacagtggggttgagggtgta-aa-tttggcttcttaccggttggag-ggggt Opossum ====================================================================== Chicken ====================================================================== X. tropicalis ====================================================================== Rat g--ctc--atagctg------------agggtagagtt----tctcgggcaaaaataatgt------ctt Mouse gttttt--atagctg------------agggtagagtt----cctcgggcaaaagtaatgt-ttttcctt Prairie vole g--ctc--atagctg------------ggggcagagtt----cctcaaacaaaagtagtgt-cttttctc Guinea pig g--agc--agggctg------------aggacggaggcagagattaggaataaagtggcgt-----actt Rabbit g---gc--agcgccg------------cgggcggagcagagctctcgggcgaattttctgt--------- Human g--agc--agagcgg---gggggg-caggggcagatgt----tttagggatgcagcgtcctgcttttctc Chimp g--agc--agagcgg---gggtgg-caggggcagatgt----tttagggatgcagcgtcctgcttttctc Rhesus g--agcagagagcggggtggggga-caggggcagatgt----tttagggatggagcgtcctgcgtttctc Tarsier g-------agaaaga----------------------t----tttagggataaggtggcctacttttctc Dog g--ggc---gaggcg------ggatcggaggcagaggt----tttaggggtaaagt-acgcaccgtt--- Panda g--ggc--agaggtg------gga-cggaggcagagat----tttaggggtaaagt-actcacctttctc Cat g--ggc--agaggcg------gga-cggaggcaga--t----tttaggggtaaagt-acgcacctttcca Cow a--ggc--agaaatg------ggagcggaagcaaa-ca----tttgggggtaaagtggcgtatctttcta Opossum ====================================================================== Chicken ====================================================================== X. tropicalis ====================================================================== Rat ctgagggatttgagaacgggc---atggggc----ctcg---gttcttgagttccggagaggggacagct Mouse ctggggtatttgagatcgggc---ttggggcctcgctcg---gatcttgagttccggagaggggacagct Prairie vole ttgaggtgtttgagaacaggc---gtggggc----cttggacgatcatgagttccggag-ggggacagct Guinea pig ttgaggggttcgagtacggat---gtggggcctttaccg---ggtcgtgagttctggagagaggacatct Rabbit --gatgagcgtgggaccggcc---ccggggcctctggcg---gaccctgagtccgcgagggccgccagct Human ctgatgagtttgagaacgggc---gtggggcctttgacg---catcgtgacttcgggagaggggacagct Chimp ctgatgagtttgagaacgggc---gtggggcctttgacg---catcgtgacttcgggagaggggacagct Rhesus ctgatgagtttgagaacgggc---gtggggcctttgacg---catcgtgacttcgggagaggggacagct Tarsier gtgatgaatttgagaacgggc---ttggggcctttgacg---gatcacgagttcgggagaggggacaacg Dog ctgacgagtttgaggatgggc---atggggccttttacg---ggtcctgagttc--gagggaaggca-ct Panda ctgatgagtttgaggacgggc---atggggcctttgacg---gatcctgagttcaagagggaaggcagct Cat ccgatgagattgagggcgggc---gtggggcccttgatg---gagcctaagttcggaagagaaggtagct Cow ctgattag-ttgcgaagggactcattggggcctttgacg---gatcctga-ctcgggagaggggacagct Opossum ====================================================================== Chicken ====================================================================== X. tropicalis ====================================================================== Rat ttattccataatgggtg Mouse ttattccataacgggca Prairie vole ttgttccctaacgggcg Guinea pig taaacacataacggggg Rabbit ctgtgagagaacgggca Human ttatcagataacg---- Chimp ttatcagataacg---- Rhesus ttatcagataacg---- Tarsier ttatcacttaac----- Dog tgatcagttaatgagc- Panda ttatcggttaatgggc- Cat ttgtcagataataggc- Cow ttatcagataacaggg- Opossum ================= Chicken ================= X. tropicalis ================= Inserts between block 23 and 24 in window B D Guinea pig 158bp Alignment block 24 of 66 in window, 80057414 - 80057450, 37 bps B D Rat taaga-ctcttctaggtaccgaggcttgcggaaatgaa B D Mouse tgaga-ctctccgaggtcctgagtcttgtggaaaggaa Prairie vole tggga-ccctcttaggtactgagtcttgtgaaaatg-a B D Rabbit -gcgg-ctcctccgcgtcatcag-ctcgctggagtgaa B D Human ---------ccctggg---------------------- B D Chimp ---------ccctggg---------------------- B D Rhesus ---------cgctggg---------------------- B D Dog cggga--tttccccgataatgagtctcgctgaaatgga B D Panda tggga--tttcccagagaattagtcttcctgaaatgga B D Cat taggagctttcccagagaattaatcttattgaaataga B D Cow tgggc--tttcccaaataagcaatcttattgaactgaa B D Guinea pig ====================================== B D Opossum ====================================== B D Chicken ====================================== B D X. tropicalis ====================================== B D Tarsier -------------------------------------- Inserts between block 24 and 25 in window B D Rabbit 933bp Alignment block 25 of 66 in window, 80057451 - 80057462, 12 bps B D Rat ccgtaaaggaaa B D Mouse ccataaagggaa Prairie vole ctgtaagaggaa B D Dog ttttaaggggaa B D Panda ttttaaggggaa B D Cat ttttaaggggaa B D Cow ttttaagaggaa B D Guinea pig ============ B D Rabbit ============ B D Rhesus ------------ B D Chimp ------------ B D Human ------------ B D Opossum ============ B D Chicken ============ B D X. tropicalis ============ B D Tarsier ------------ Inserts between block 25 and 26 in window B D Dog 1190bp Alignment block 26 of 66 in window, 80057463 - 80057463, 1 bps B D Rat a B D Mouse a Prairie vole a B D Panda g B D Cat g B D Cow g B D Dog = B D Guinea pig = B D Rabbit = B D Rhesus - B D Chimp - B D Human - B D Opossum = B D Chicken = B D X. tropicalis = B D Tarsier - Inserts between block 26 and 27 in window B D Panda 1bp Alignment block 27 of 66 in window, 80057464 - 80057464, 1 bps B D Rat a B D Mouse g Prairie vole g B D Cat a B D Dog = B D Guinea pig = B D Rabbit = B D Rhesus - B D Cow - B D Chimp - B D Human - B D Opossum = B D Chicken = B D X. tropicalis = B D Panda = B D Tarsier - Inserts between block 27 and 28 in window B D Cat 1352bp Alignment block 28 of 66 in window, 80057465 - 80057581, 117 bps B D Rat ctgagtctgatggcacatgcctagaatccc--------------------------aa-gcctagagagg B D Mouse ctgagtctgatggcacatgcctggaatccc--------------------------ag-gcctcgagagg Prairie vole ctgagcctggtggtacatgcctagaatccc--------------------------ag-gct----gatt B D Human ctgggcgcgggggctcattcctgtgatccc--------------------------agcactttagtagg B D Chimp ctgggcgcgggggctcatgcctgtgatccc--------------------------agcactttagtagg B D Rhesus ctgggcgcggggactcatgcctgtgatccc--------------------------agcattttagtagg B D Tarsier ---gggtcgggatctttcccacgtaattcaccctgtcgaagtgaatgtcaagcgggagcgattttacaaa B D Cow ----------------------------------------------------------cgtttttacgaa B D Cat ====================================================================== B D Dog ====================================================================== B D Guinea pig ====================================================================== B D Rabbit ====================================================================== B D Opossum ====================================================================== B D Chicken ====================================================================== B D X. tropicalis ====================================================================== B D Panda ====================================================================== Rat ctgagtcaggagtatcgctag------------ttggtggtcagccttgaccagcttcatagcgtgt--- Mouse ctgatgcaggaggttcgctag------------ttg-------gccttggccagcttcatagcgaga--- Prairie vole ctgaggcaggaggtt-gcgag------------ttcgtggccagccttgg---gcttcatagcgaga--- Human ccaaggc-ggagcatcgctggaacac-aggag-ttcgagactagcctag----gcaacatagcgagaccc Chimp ccaaggc-ggagcatcgctggaacac-aggag-ttcgagactagcctag----gcaacatagcgagaccc Rhesus ccaaggcgggagcatcgctagaacac-aggagtttcgagactactctag----gcaacatagcgagaccc Tarsier taaagat---------cttgggggag-gggag-tgcg--------------------------------- Cow ttaaaaa---------cctgggagatgaggag-tacg----------------gacttgtag-------- Cat ====================================================================== Dog ====================================================================== Guinea pig ====================================================================== Rabbit ====================================================================== Opossum ====================================================================== Chicken ====================================================================== X. tropicalis ====================================================================== Panda ====================================================================== Rat ccgcttacaaaagtaatag Mouse ccgcttccaaaagtaatag Prairie vole ccgtttccaaaagtagtag Human ccgtctctacaaaaaaaaa Chimp ccgtctctac-agaaaaaa Rhesus ccgtctctac--aaaaaaa Tarsier ------------------- Cow ------------------- Cat =================== Dog =================== Guinea pig =================== Rabbit =================== Opossum =================== Chicken =================== X. tropicalis =================== Panda =================== Inserts between block 28 and 29 in window B D Human 8bp B D Chimp 8bp B D Rhesus 8bp Alignment block 29 of 66 in window, 80057582 - 80057610, 29 bps B D Rat taattttatatagaagtggtcttaatgga B D Mouse taattttaaatggaagtggtctt-atgaa Prairie vole taattttaaatgggaatggtctt-atgaa B D Guinea pig cgattttaagggggagctattttaaggaa B D Human taattatgaaaaaca--tgttttaaacga B D Chimp taattatgaaaaaca--tgttttaaacga B D Rhesus taattatgaaaaaca--tattttaaacga B D Tarsier cagttttggaagtaa--tgacttg----- B D Cow ----------gaaaagtggtcttaagg-- B D Cat ============================= B D Dog ============================= B D Rabbit ============================= B D Opossum ============================= B D Chicken ============================= B D X. tropicalis ============================= B D Panda ============================= Alignment block 30 of 66 in window, 80057611 - 80057615, 5 bps B D Rat tgaag B D Mouse taaag Prairie vole taaag B D Guinea pig taaat B D Human taacg B D Chimp taacg B D Rhesus taacg B D Panda gaaga B D Cow taaga B D Cat ===== B D Dog ===== B D Rabbit ===== B D Opossum ===== B D Chicken ===== B D X. tropicalis ===== B D Tarsier ----- Inserts between block 30 and 31 in window B D Rhesus 2575bp Alignment block 31 of 66 in window, 80057616 - 80057622, 7 bps B D Rat agct--tgg B D Mouse agct--tgg Prairie vole agct--tgg B D Guinea pig tgccggcgg B D Human ggag--tgg B D Chimp ggag--tgg B D Tarsier aggt--tgg B D Panda acct--ggg B D Cow ggct--tag B D Cat ========= B D Dog ========= B D Rabbit ========= B D Rhesus ========= B D Opossum ========= B D Chicken ========= B D X. tropicalis ========= Inserts between block 31 and 32 in window B D Human 2588bp B D Chimp 2bp B D Panda 1bp Alignment block 32 of 66 in window, 80057623 - 80057645, 23 bps B D Rat cggaga----aggaagtactattagaa B D Mouse cgggga----aggaagaactgttagaa Prairie vole ctggagttatagggaattgtgttaaaa B D Guinea pig caggaa----agtgaagtctattatta B D Chimp ctagat----aattagtcctattgaaa B D Tarsier --------------ggacttatccgga B D Panda aagggg----agtgcggagttttagaa B D Cow ctggag----acaattggcttttcga- B D Cat =========================== B D Dog =========================== B D Rabbit =========================== B D Rhesus =========================== B D Human =========================== B D Opossum =========================== B D Chicken =========================== B D X. tropicalis =========================== Inserts between block 32 and 33 in window B D Chimp 2255bp B D Tarsier 3bp Alignment block 33 of 66 in window, 80057646 - 80057958, 313 bps B D Rat atagtaaa--------tagagac--------------gtatgggacttaaccaggataaattagg----- B D Mouse atagt-------------gaaaa--------------gtatgggacgtaaccaggataaattaga----- Prairie vole atagtgaaaggctctctaaaaaaaaataataataatggtgagggacttaaccaggataaattagagatca B D Guinea pig ataacgac----------ttgaa--------------gtaagggattt-atctggagaatttaagctgct B D Tarsier -----------------------------------------------------------attgagctgga B D Panda ataacgct----------ttgag--------------gtacgggactt-acccggacaatttgagctgga B D Cow -------------------tcac--------------atccgccattt-gtacggataac---------- B D Cat ====================================================================== B D Dog ====================================================================== B D Rabbit ====================================================================== B D Rhesus ====================================================================== B D Chimp ====================================================================== B D Human ====================================================================== B D Opossum ====================================================================== B D Chicken ====================================================================== B D X. tropicalis ====================================================================== Rat --------acttttgaacctaatt---agagattgtcagag-tagcaggctactacaatg---------- Mouse --------------gaacctaact---agagactgtcagag-tagcagggtactacagtggtttg----g Prairie vole gacaggtggctttttgacctaatcaagagagaccgtcagag-tagcaagctactgaggaattttg----g Guinea pig ggcgggtgacttt------tcttt---tgcgactgtgaca--cagtgagccactaaagtgagtt------ Tarsier gacgggtggctcttttacctgatt---cgggactttaaaggataacgagtcactggcatgatttt----g Panda ggtggttggcttt-tcacctcatt---cgcgactttttcggctcacgagtcactgtaatgactttcctga Cow ----------------------------------------------gagttatgggggtgatttt----a Cat ====================================================================== Dog ====================================================================== Rabbit ====================================================================== Rhesus ====================================================================== Chimp ====================================================================== Human ====================================================================== Opossum ====================================================================== Chicken ====================================================================== X. tropicalis ====================================================================== Rat -----gtttattcattgagcggatattatgtagac----tgtaagtt---------------------ag Mouse tgcgtgtttattcattgagcatatactatgtagactgcttgtaagtt--------------------aag Prairie vole tgt--gtttattcattgagcagatgttacatagcctgtttataggtt--------------------aag Guinea pig -----tgctgtttgtttggtagatattacgttgagtgttcacgtgtcgggcactgcattgatcacatggg Tarsier cga--atgtattcgttccgcaggtgtgccgttgagtgctcatgtatcaggcactgctttagacacgtagg Panda ttg--attgatttactcagcaagtatt-tattgagcgctcccgcatcgggcactgctttagacatgtggg Cow ctt--atatattcactcaacagttatt-tattgagtgtttgggtattagg--ctgctttagacacataga Cat ====================================================================== Dog ====================================================================== Rabbit ====================================================================== Rhesus ====================================================================== Chimp ====================================================================== Human ====================================================================== Opossum ====================================================================== Chicken ====================================================================== X. tropicalis ====================================================================== Rat aca-cat-ggtaaatagaaggtccttgctaccaagga-----aaaaa--aatctctcagg-gcttataaa Mouse aca-cat-ggtaaataaaaggtccttgcctccaaggg--ggtggggg--aatctccctggtgcttgtaaa Prairie vole aca-cac-ggtgagtaaaagacccttgccaccaagggaagaaaaaga--aatctcagtgggccttgtaaa Guinea pig ata-catcagggaatgaaaggtcctcatccccgagaa-----aaaca--ttttctattatgggttatgag Tarsier ata-catcagtgaatgaaatctcctggtcccaaagaa----acaaaa--tctttagttacagtttatggg Panda ata-catcattgaatacca--cccccgcctcctaaga---aaaaaaacctcccctgctgcagcttatggg Cow ttattatcactgaattact--ccactttccccaagga---aaaaaaa--tcctcttctacatcttacggg Cat ====================================================================== Dog ====================================================================== Rabbit ====================================================================== Rhesus ====================================================================== Chimp ====================================================================== Human ====================================================================== Opossum ====================================================================== Chicken ====================================================================== X. tropicalis ====================================================================== Rat aagaatccaataggaaagcca----taga-------gtaataaacaag-taca-tacagtatgtcttaga Mouse aagagtggagtaggaaagcca----taga-------gtaataaatagg-taca-taca-----ccttaga Prairie vole aggaatgggttaggaagacca----------------taatgaacagg-tatg-tacagcgtgt------ Guinea pig gggagcaaagtactcaggcca----taga-------ataataa--agg-aata-tatagcgtgtcatg-- Tarsier gggaa-----gaggcaggcgataagtaga-------atcataaacaagctaag-tatatgatgtgttagg Panda gtggg---aaaaggcaggcaa----tgaatacgctgataataaacatg-tgaagcatgtggcgtgttagg Cow atggg---aagaggcaggcag----gaaacgtgctggtaataaatacg-taaattctagaatgtgttagg Cat ====================================================================== Dog ====================================================================== Rabbit ====================================================================== Rhesus ====================================================================== Chimp ====================================================================== Human ====================================================================== Opossum ====================================================================== Chicken ====================================================================== X. tropicalis ====================================================================== Rat tgatcaggagtgtgaat----gg--agaattgagtaggaaagaaata---------------acaccagt Mouse taatcag--gtttggat----gg--agaattgagcaggaaagatata---------------atgccagt Prairie vole tagccag-agtgttaat----ga--agaagttg----------------------------------agt Guinea pig tgtccagggctgttaat----aaacatagtttagtaggacagcaacactgggaag-------accacagt Tarsier tgatggg-gccgtgaatccagaa--acagctgagcagggtgaaaacagtggccaattcctataacttaat Panda tgactagagctgtgagtaaataa--acaatagagcagggtaaaaacaatggggaatgcca--gtttgaga Cow -gaatagggttgtgaataaagaa--ataacagagcagggt-aaaacagtgtggaatgtcac-ttttgaga Cat ====================================================================== Dog ====================================================================== Rabbit ====================================================================== Rhesus ====================================================================== Chimp ====================================================================== Human ====================================================================== Opossum ====================================================================== Chicken ====================================================================== X. tropicalis ====================================================================== Rat a-g-----------------gtagcacagaagta Mouse a-g-----------------gtagcacagtagga Prairie vole a-a-----------------ctagctcaaaagga Guinea pig gta-----------------gtgtcacagaagga Tarsier a-a-----------------ctagcacagcagga Panda g-a-----------------gggtaacttaataa Cow g-acagaacacataaaggagggaacacttgagca Cat ================================== Dog ================================== Rabbit ================================== Rhesus ================================== Chimp ================================== Human ================================== Opossum ================================== Chicken ================================== X. tropicalis ================================== Inserts between block 33 and 34 in window B D Panda 2bp B D Cow 248bp Alignment block 34 of 66 in window, 80057959 - 80057986, 28 bps B D Rat ----ttgggcattgaaagcccaatacttgggc B D Mouse ----t---gcattgaaagcccagttcttggga Prairie vole ----c---accctgaaagcgcagtactcgggc B D Guinea pig ----c---ctattgagaaggaaaagcttgagc B D Tarsier ----c---acatcgggaaggtgacacttgagc B D Panda aggac---acattgagaaagcaacagttgagc B D Cat ================================ B D Dog ================================ B D Rabbit ================================ B D Rhesus ================================ B D Cow ================================ B D Chimp ================================ B D Human ================================ B D Opossum ================================ B D Chicken ================================ B D X. tropicalis ================================ Inserts between block 34 and 35 in window B D Tarsier 1155bp B D Panda 308bp Alignment block 35 of 66 in window, 80057987 - 80058131, 145 bps B D Rat -------------------tggggatt------------tagctt--------------agtggacagag B D Mouse -------------------tgcagatt------------tagctc--------------agtggacagag Prairie vole -------------------tggagtta------------taggac--------------ag-----agag B D Guinea pig aaggaagaaagtgagaaagtgaagcttccagataactggtagttccaggcatgggtaaaagcaaacagag B D Cat ====================================================================== B D Dog ====================================================================== B D Rabbit ====================================================================== B D Rhesus ====================================================================== B D Cow ====================================================================== B D Chimp ====================================================================== B D Human ====================================================================== B D Opossum ====================================================================== B D Chicken ====================================================================== B D X. tropicalis ====================================================================== B D Panda ====================================================================== B D Tarsier ====================================================================== Rat tactta---------cctactgtgggccctgggtttggtcctcagccacacacagactaga--------- Mouse tactta---------cctactgtgggtactgggtttggtccttaaccacacacaaactagacatagtggc Prairie vole tacttg---------gctactatgggcactgggttcagccctcagcgccacacaaactgggcctggtggc Guinea pig gccttaagatgaaagtttgcctcttgtcttgagaagaccacctaggaagccactggctaga-acaatgtg Cat ====================================================================== Dog ====================================================================== Rabbit ====================================================================== Rhesus ====================================================================== Cow ====================================================================== Chimp ====================================================================== Human ====================================================================== Opossum ====================================================================== Chicken ====================================================================== X. tropicalis ====================================================================== Panda ====================================================================== Tarsier ====================================================================== Rat --------tgtaaccccagtatcctggaggcagagacagacaagtctgagttccaggggcaggtctattt Mouse acgt-gcctgtactcccaatactcaggaggcag----agacaagtctgagttct-ggggcagccaggctt Prairie vole acag-gcctgtaatcccagcactcttgaggcagagatgga-gagtctaagtccc-aggccagccaggctt Guinea pig acagagcctgcagcagtgtgagagaggaggcaggtgtaaagcattgtgaaagct----ttggttttcctt Cat ====================================================================== Dog ====================================================================== Rabbit ====================================================================== Rhesus ====================================================================== Cow ====================================================================== Chimp ====================================================================== Human ====================================================================== Opossum ====================================================================== Chicken ====================================================================== X. tropicalis ====================================================================== Panda ====================================================================== Tarsier ====================================================================== Rat atacag Mouse ctacag Prairie vole acacgg Guinea pig ttacac Cat ====== Dog ====== Rabbit ====== Rhesus ====== Cow ====== Chimp ====== Human ====== Opossum ====== Chicken ====== X. tropicalis ====== Panda ====== Tarsier ====== Alignment block 36 of 66 in window, 80058132 - 80058154, 23 bps B D Rat ggagac-actgttgtggggtggga- B D Mouse tgaga----tgttgtggggtgggg- Prairie vole tggga----tgttgtgggg------ B D Guinea pig tgagatgggagctatggaaaggct- B D Cow -gggcaaactgttggggagcgtggg B D Cat ========================= B D Dog ========================= B D Rabbit ========================= B D Rhesus ========================= B D Chimp ========================= B D Human ========================= B D Opossum ========================= B D Chicken ========================= B D X. tropicalis ========================= B D Panda ========================= B D Tarsier ========================= Inserts between block 36 and 37 in window B D Cow 18bp Alignment block 37 of 66 in window, 80058155 - 80058174, 20 bps B D Rat tggaag-------------------------------------a-----------------gaaatggcc B D Mouse cggaggttcatggagagagatgattgaagtttaggttgcggata-----------------gaaagggcc Prairie vole -----atccctggagagagatgatggaagttgagcccatggata-----------------gaaatggcc B D Guinea pig tcaaag-------ggtgacatgatgtggtttaggttttagcacagtccttcacactgctctgtgacagac B D Panda ---------taggagagaggtgatggagg----------------------------------------- B D Cow ---------taggaaagagatgatggagg----------------------------------------- B D Cat ====================================================================== B D Dog ====================================================================== B D Rabbit ====================================================================== B D Rhesus ====================================================================== B D Chimp ====================================================================== B D Human ====================================================================== B D Opossum ====================================================================== B D Chicken ====================================================================== B D X. tropicalis ====================================================================== B D Tarsier ====================================================================== Rat aaat Mouse aag- Prairie vole agg- Guinea pig agat Panda ---- Cow ---- Cat ==== Dog ==== Rabbit ==== Rhesus ==== Chimp ==== Human ==== Opossum ==== Chicken ==== X. tropicalis ==== Tarsier ==== Inserts between block 37 and 38 in window B D Panda 26bp B D Cow 19bp Alignment block 38 of 66 in window, 80058175 - 80058177, 3 bps B D Rat ttt B D Mouse gtt Prairie vole ttc B D Guinea pig tgt B D Dog ttc B D Panda ttc B D Cow ttc B D Cat === B D Rabbit === B D Rhesus === B D Chimp === B D Human === B D Opossum === B D Chicken === B D X. tropicalis === B D Tarsier === Inserts between block 38 and 39 in window B D Cow 5bp Alignment block 39 of 66 in window, 80058178 - 80058229, 52 bps B D Rat tggacatatca-tggaagcagatgacaagataaga---cgacagagtga--------ggtttga B D Mouse tggatgtacca-tggtggcagatgacaagatataa---ggatagagtaa--------ggtttga Prairie vole tggatacgttg-tcaaggcagataacaatg------------------------------ttga B D Guinea pig cagaagtgtgagtggaagcaaagagaccggtaaaactccgagagagggatgatg-atgattcca B D Dog tgggtatattt-tagaggcagatgacagaatttgc---tgac--attga--atgtaggatgtga B D Panda taggaatattt-taga-gcagatgacaggatttgc---tgacagatgga--atgcaggatgtga B D Cat tggatgtattt-tagaagcagatggcagggtttgc---cgacagattga--atggcgggtgtga B D Cow ctgataggttt-tagtggcagatgactggattttc---tgacagactga--atgtaggatgt-- B D Rabbit ================================================================ B D Rhesus ================================================================ B D Chimp ================================================================ B D Human ================================================================ B D Opossum ================================================================ B D Chicken ================================================================ B D X. tropicalis ================================================================ B D Tarsier ================================================================ Inserts between block 39 and 40 in window B D Mouse 3bp Prairie vole 3bp B D Guinea pig 9bp Alignment block 40 of 66 in window, 80058230 - 80058310, 81 bps B D Rat -----aaga----atcaggtgccaggcat--gatggtgagccc--------------------cctgtaa B D Mouse -----aaga----atcaactgccaggcat--gatggtgag-cc--------------------tctgtca Prairie vole -----aaga----atccagtgccgggcat--gacagtgga-cc--------------------cctgtaa B D Guinea pig -----aagaaattatcggagtctgggtattcattggtagc-ccagttcacgtactccattctttctataa B D Human -----aaaa----atta---gctgggcgt--ggaggtggt-gc-----------------atgcctgtag B D Chimp -----aaaa----atta---gctgggcgt--ggaggtggt-gc-----------------atgcctgtag B D Dog gagagaaga----gtcaagt--------t--gatatcagg--g--------------------tttctgc B D Panda gagagaaga----gtcaagt--------t--ggtatcaga-ct--------------------tttttgc B D Cat gagagaaga----gtcaagt--------t--gataccaga--g--------------------tttttgc B D Cow gagagaaga----gtcaagt--------t--gacagcagg--g--------------------cttttgc B D Rabbit ====================================================================== B D Rhesus ====================================================================== B D Opossum ====================================================================== B D Chicken ====================================================================== B D X. tropicalis ====================================================================== B D Tarsier ====================================================================== Rat tctcag------------------------------accttgggtgatg---------------gagtca Mouse tctcag------------------------------accttaggcagtg---------------gagtca Prairie vole tctcag------------------------------agtttgggaggtg---------------gagtca Guinea pig ttctggtcaaaaactgaattagacaagaaccaaatcaaattcagtggta---------------ggttca Human tcccag-----------------------------ctcctcaggaggct---------------gaggca Chimp tcccag-----------------------------ctcctcaggaggct---------------gaggca Dog tcaagg------------------------------aactagaatgatg---------------gagatg Panda tcgagg------------------------------agctagaaggatg---------------gagacg Cat tcaagg------------------------------aactagaaggatg---------------gagaca Cow tcaaag------------------------------aaccagagggatggagtcaccattgacagagatg Rabbit ====================================================================== Rhesus ====================================================================== Opossum ====================================================================== Chicken ====================================================================== X. tropicalis ====================================================================== Tarsier ====================================================================== Rat -----ggagaattga--gaattca Mouse -----ggagaattga--gaattca Prairie vole -----ggagaactga--gaattga Guinea pig atgttgggga--------aattca Human -----ggagaatcgcttgaaccca Chimp -----ggagaatcgcttgaaccca Dog ------------------------ Panda ------------------------ Cat ------------------------ Cow ------------------------ Rabbit ======================== Rhesus ======================== Opossum ======================== Chicken ======================== X. tropicalis ======================== Tarsier ======================== Inserts between block 40 and 41 in window B D Human 8bp B D Chimp 8bp Alignment block 41 of 66 in window, 80058311 - 80058316, 6 bps B D Rat ---aggtca B D Mouse ---aggtca Prairie vole ---aggtca B D Guinea pig ---attcca B D Human ---aggtt- B D Chimp ---aggtt- B D Tarsier ---aggtt- B D Dog aggaag--- B D Panda aggaag--- B D Cat gggaag--- B D Cow aggaag--- B D Rabbit ========= B D Rhesus ========= B D Opossum ========= B D Chicken ========= B D X. tropicalis ========= Inserts between block 41 and 42 in window Prairie vole 139bp B D Guinea pig 1bp Alignment block 42 of 66 in window, 80058317 - 80058347, 31 bps B D Rat acagtggctggacgaggtt---tggttaat-----------gagc B D Mouse gcggtgggtggaagaggtt---aggtagat-----------gagc Prairie vole acagtaggtggaagaggtttggaggttgat-----------gaac B D Guinea pig aaggtagatag-caagatttgcctatagctt---tgacatagggt B D Human ---gcagtgagccgagatc---acatcact-----gcgctccagc B D Chimp ---gcagtgagccgagatc---acaccact-----gcgctccagc B D Tarsier ---ctgggtggctggg-------------------------cgat B D Dog gctgtggaaagagtaggtt---tgagtgattgggagatctggagc B D Panda gctatggatggagtaggtt---ggggtggttgggagatcgggagc B D Cat actctggatagagtaagtg---ggggcggttgggagatctggagc B D Cow gctgtggatagtataagtt---ggggtta-tgggcggtctggagt B D Rabbit ============================================= B D Rhesus ============================================= B D Opossum ============================================= B D Chicken ============================================= B D X. tropicalis ============================================= Alignment block 43 of 66 in window, 80058348 - 80058363, 16 bps B D Rat tggagca----------------gg-ctaactt B D Mouse cggggca----------------gg-ctaccat Prairie vole tggagca----------------gg-ccaactt B D Guinea pig ctgagaa----------------ga-caagaat B D Human ctgggcaaca-------gatcaaga-ctc---- B D Chimp ctgggcaaca-------gagcaaga-ctc---- B D Tarsier ctgg-------------------ag-ctc---- B D Dog tcaactgaggat-----gtatacgg-tt----- B D Panda tcaaatgaggat-----gtgaaagg-tt----- B D Cat tcaaccgacggt-----gcgtaagg-tt----- B D Cow tcagtctaggac-----atgtgaggatt----- B D Platypus -----------tggcggagtcggga-tt----- B D Rabbit ================================= B D Rhesus ================================= B D Opossum ================================= B D Chicken ================================= B D X. tropicalis ================================= Inserts between block 43 and 44 in window B D Human 15bp B D Chimp 15bp B D Tarsier 19bp Alignment block 44 of 66 in window, 80058364 - 80058404, 41 bps B D Rat g---gaa---atgtctctc---------------------ctgcctccag-----------------aga B D Mouse g---gaa---atgtctctc---------------------ctgcctccag-----------------aaa Prairie vole g---gaa---agatctctc---------------------tcacctccag-----------------aga B D Guinea pig gtcaaga---gtatttacctagaaaactagggagatgaagttgctgtcag-----------------tgg B D Human ---aaaa---atgtctgtt---------------------aggcatctag-ctgatgatactc----aga B D Chimp ---aaaa---aagtctgtt---------------------aggcatctag-ctgatgatactc----aga B D Rhesus ---gaaa---atgtctgtt---------------------aggcatccag-ctggtgatactc----aga B D Tarsier ---gaaa---atgcctgtt---------------------agacatccag-ttggtgattccaggagaga B D Dog ---ggaa---atgtctatt---------------------cagcatccag-ctggtgatgccatgcaaga B D Panda ---ggaa---atgtctctt---------------------aagcctccga-gtggtgatgccaagtgaga B D Cat ---ggaa---atgtctatt---------------------aagcatctga-gctgtgatgccaagcgaga B D Cow ---ggaa---atatccatt---------------------aggcatccaa-gtggtgataccaagagaga B D Platypus ---ggaacccatgaccttc---------------------tgactcccaggccggtggt--------cga B D Rabbit ====================================================================== B D Opossum ====================================================================== B D Chicken ====================================================================== B D X. tropicalis ====================================================================== Rat ag-----------actgta-------------cc-----agg-aa Mouse ag-----------actgca-------------cc-----aga-aa Prairie vole aa-----------actgag-------------cc-----agg-ga Guinea pig aga--tggggagtactgtgggtagagtgggtttc-----agt-gt Human ag-----------gctgaa-------------ca---ggagg-ac Chimp ag-----------gctgaa-------------ca---ggagg-ac Rhesus ag-----------gccaaa-------------c------agg-ac Tarsier ag-----------gctgag-------------ca---ggagg-at Dog ggg----------actgag-------------ca---ggggg-gt Panda ggg----------actgag-------------cc---ggagg-gt Cat ggc----------gctgag-------------ca---ggagg-gt Cow gg-----------actgag-------------ta---ggaggaga Platypus acggctatgccatgctgag-------------cctttgggaa-gt Rabbit ============================================= Opossum ============================================= Chicken ============================================= X. tropicalis ============================================= Alignment block 45 of 66 in window, 80058405 - 80058434, 30 bps B D Rat --gggcattt-gggggccaggctggggagacac B D Mouse --ggg--------------ggctggggagacac Prairie vole --ggg-tgtt-tggggccaggttgaggggacac B D Guinea pig --ggg-tgtt-ggcagcaagattggggggacaa B D Human --aga-tgtggtgggacaaggttggggagacac B D Chimp --aga-tgtggtgggacaaggttggggagacac B D Rhesus --gga-tgtgatgggacaaggctggggagacat B D Tarsier --ggg-tgt--tgggtaaagattggggaggcac B D Dog --ggg-t-----------gggttggggagaca- B D Panda --ggg-tatgttggggaaaggttggggagacac B D Cat --ggg-cgtgttaggggaaggttgaggagacgc B D Cow --ggg-tatgt---------gtcggggagacac B D Platypus --gga-ctctgtgaacccaagc-gggaaatcaa B D Chicken gggga-tatggggacatggagctatggggacat B D Rabbit ================================= B D Opossum ================================= B D X. tropicalis ================================= Alignment block 46 of 66 in window, 80058435 - 80058466, 32 bps B D Rat tggacaa---------------tgtagctttggt--cacttatgctt--------------------cc B D Mouse tggacag---------------tgtggctttgat--cacgtacattt--------------------cc Prairie vole tggaca-----------------gtggctttgat--cgctcacgctc--------------------cc B D Guinea pig cacaaa--------------------gccaggac--cagccatgctc--------------------tc B D Human tgaagc----------------caaggccctgat--cacccatcctcacagctccagcctctcaactcc B D Chimp tgaagc----------------caaggccctgat--cacccatcctcacagctccagcctctcaactcc B D Rhesus tgaggc----------------tgaggccctgac--cacccatcctcacag--------------ctcc B D Tarsier tgaggg----------------catggccctgac--cacccacactc--------------------cc B D Dog ---------------------------tcatgtgaccacccacgctc-tagctctggg----------- B D Panda caagtg----------------cgaggccatgggaccacgcacgctc-cagcactggg----------- B D Cat tgagtg----------------caaggccatgtggccacccatgctc-cagctctggg----------- B D Cow cgaggg----------------agaggccatgag--caccca-------ggctgtggg----------- B D Platypus ttctcc----------------cgtacccat-at--ctcccatcaac---------------------- B D Chicken tgggacagcgg--ggggccccccagggtgcaggc--cgccctcag------------------------ B D Zebrafish --------tggccgatgtaaattttagcccttta--tgcagac-------------------------- B D Rabbit ===================================================================== B D Opossum ===================================================================== B D X. tropicalis ===================================================================== Alignment block 47 of 66 in window, 80058467 - 80058474, 8 bps B D Rat -----aacctgaa B D Mouse -----aacttgaa Prairie vole -----aatgt-ca B D Guinea pig -----agcct-ca B D Human -----ag------ B D Chimp -----ag------ B D Rhesus -----ag------ B D Tarsier -----aa------ B D X. tropicalis -----------aa B D Zebrafish atgctaa------ B D Cat ------------- B D Dog ------------- B D Rabbit ============= B D Cow ------------- B D Opossum ============= B D Chicken ------------- B D Platypus ------------- B D Panda ------------- Inserts between block 47 and 48 in window B D X. tropicalis 6bp Alignment block 48 of 66 in window, 80058475 - 80058478, 4 bps B D Rat cccg B D Mouse ccca Prairie vole tcca B D Guinea pig ccca B D Rabbit ctcc B D Human cctc B D Chimp cctc B D Rhesus cctc B D Tarsier ctcc B D Dog --cc B D Panda -ccc B D Cat -ccc B D Cow -cct B D Platypus ctta B D Chicken gcca B D X. tropicalis gcca B D Opossum ==== B D Zebrafish ---- Inserts between block 48 and 49 in window B D Guinea pig 4bp Alignment block 49 of 66 in window, 80058479 - 80058689, 211 bps B D Rat tc-tcac-----cccccggg--------ttctctatccaggagtctcctcaataaacccaagagtgagat B D Mouse tc-tca------cccctggg--------ttctctatccaggagtctcctcaataaacccaagagtgagat Prairie vole tc-tca------cccatggc--------ctctctattcaggagtctcctcaataaacccaagagtgagat B D Guinea pig tc-tgt------ct--------------ttgcctgttcaggagcctccttaacaagcccaagagtgagat B D Rabbit cc-tca------cccgcgggtccc--tcctcccccgtcaggagcctcctcaacaagcccaagagcgagat B D Human tc-tca------cttattggttccatgtttgtccatgcaggagcctcctcaacaagcccaagagtgagat B D Chimp tc-tca------cttattggttccatggttgtccatgcaggagcctcctcaacaagcccaagagtgagat B D Rhesus tc-tca------cttgtgggttccatgtttgtccatgcaggagcctcctcaacaagcccaagagtgagat B D Tarsier tc-tca------cctatgggttccatacttgt-cattcaggagcctcctcaacaagcccaagagtgagat B D Dog tc-tca------cctacgggttccatgcttgccc-ctcaggagcctcctcaacaaacccaagagtgagat B D Panda cc-tca------cctacgggtaccatgcttgcccactcaggagcctcctcaacaagcccaagagtgagat B D Cat tcttca------cctaccgcttccatacttgccccctcaggagcctcctcaacaagcccaagagtgagat B D Cow tc-tca------cctctgggttccatacttgtcttctcaggagtctcctcaacaagcccaagagtgagat B D Opossum ------------tctctgtgtctgtgcactgtcc--ccaggagtctcttaaacaagcccaagagcgagat B D Platypus ------------------------tgtccaccccatccaggagtctcctaaacaagcccaagagcgagat B D Chicken ------ttgacccccctgag------------ccccccaggagcctcctgaacaaacccaagagcgagat B D X. tropicalis ---tct------cacactgattctaaa----tctcttcaggagtctccttaacaagcccaaaagtgagat B D Zebrafish --------------------ctgttgaaatgtctcatcaggagtttattaaacaagcccaaatctgagat Rat gaccccagaggagctgcagaagcgggaggaggaggaattcaacacaggtcccctctcggtgctcacacag Mouse gaccccagaggagctgcagaagcgggaggaggaggaattcaacacaggtcccctctcagtgctcacgcag Prairie vole gaccccagaggagctgcagaagcgggaggaggaggaattcaacacaggccccctctcggtactcacgcag Guinea pig gaccccagaggagctgcaaaagcgggaggaggaggaatttaacacaggtccgctctcggtgctgacccag Rabbit gacccccgaggagctgcagaagcgggaggaggaggagttcaacacgggcccgctctccgtgctcacgcag Human gaccccagaggagctgcagaagcgagaggaggaggaatttaacaccggtccactctctgtgctcacacag Chimp gaccccagaggagctgcagaaacgagaggaggaggaatttaacaccggtccactctctgtgctcacacag Rhesus gaccccagaggagctgcagaagcgagaggaggaggaatttaacacgggtccactctctgtgctcactcag Tarsier gaccccagaggagctgcagaagcgagaagaagaagaatttaacacgggtccactctctgtgctcacacag Dog gaccccagaggagctacagaagcgggaggaggaagagtttaacacgggtccgctctctgtgctcacacag Panda gaccccagaggagctgcagaagcgggaggaggaggagttcaacacaggcccgctctctgtgctcacgcag Cat gacccccgaggagctgcagaagcgggaggaggaagagtttaacacgggtccgctctctgtgctcacgcag Cow gaccccagaggagctgcagaagcgggaggaggaggagtttaacacggggccactctccgtgctcacgcag Opossum gactcctgaggagctgcagaagagggaagaggaggagttcaacactggacccctgtcagtgctcacccag Platypus gaccccggaggagctgcagaagcgcgaggaggaggagttcaacacggggcccctgtcggtgctgacccag Chicken gacgccggaggagctgcagaagcgcgaggaggaggagttcaacaccgggccgctgtcggtgctgacgcag X. tropicalis gacacctgaagagctacaaaagcgagaagaggaggagttcaacacagggccactgtctgtgcttactcag Zebrafish gactccagaggagctccagaagcgagaggaggaagagtttaacaccggtccactttcagtgctcacccag Rat tcggtcaaaaacaacacgcaagtgctcattaactgtcgaaacaacaagaagctcctgggccgggtgaagg Mouse tcggtcaagaacaacacgcaagtgctcattaactgtcgcaacaacaagaagctgctgggccgggtgaagg Prairie vole tcggtcaagaacaacacacaggtgctcattaactgtcgcaacaacaagaagctcctggggcgggtgaagg Guinea pig tcagtcaagaacaacacccaggtgctcatcaactgccgcaacaacaaaaaactcctaggccgggtgaagg Rabbit tcggtcaagaacaacacgcaggtgctcatcaactgccgcaacaacaagaagctgctgggccgcgtgaagg Human tcagtcaagaacaatacccaagtgctcatcaactgccgcaacaataagaaactcctgggccgcgtgaagg Chimp tcagtcaagaacaatacccaagtgctcatcaactgccgcaacaataagaaactcctgggccgcgtgaagg Rhesus tcagtcaagaacaacacccaagtgctcatcaactgtcgcaacaataagaaactcctgggccgtgtgaagg Tarsier tctgtcaagaacaacacccaagtgctcatcaactgtcgcaacaacaagaaactcctgggacgtgtgaagg Dog tcagtcaagaacaacacccaggtgcttatcaactgccgcaacaacaagaagctcctgggccgtgtgaagg Panda tcagtcaagaacaacacccaggtgcttatcaactgccgcaacaacaagaagcttctgggccgcgtgaagg Cat tcggtcaagaacaacacccaagtgctcatcaactgccgcaacaacaagaagctcctgggccgcgtgaagg Cow tcagtcaaaaacaacactcaagtgctcatcaactgccgtaacaacaagaagctcctgggccgcgtgaagg Opossum tcagtgaagaacaacacccaggttcttatcaattgccgcaacaacaagaaactgctgggtcgagtgaagg Platypus tcggtaaagaacaacacacaggttctcatcaactgcagaaacaacaagaaactgttgggccgcgtcaagg Chicken tcggtgaagaacaacacgcaggtgctgatcaactgccgcaacaacaagaagctgctgggccgcgtcaagg X. tropicalis tctgtgaagaacaacacacaagttctgatcaactgcaggaataacaaaaagttgctaggcagagtaaaag Zebrafish tctgtgaaaaacaacacacaggtcctcatcaactgccgcaacaacaagaagctgctgggcagagtcaaag Rat cctttgacaggtggg Mouse cctttgacaggtgag Prairie vole cctttgacaggtgag Guinea pig cctttgacaggtgag Rabbit ccttcgacaggtgcg Human ccttcgataggtgag Chimp ccttcgataggtgag Rhesus ccttcgataggtgag Tarsier ccttcgacaggtgag Dog ctttcgacaggtaag Panda ccttcgacaggtgag Cat ccttcgataggtgag Cow cctttgacaggtgag Opossum cctttgacaggtggg Platypus cattcgacaggtgag Chicken ccttcgacaggtggg X. tropicalis cctttgacaggt--- Zebrafish cattcgacaggtaac Inserts between block 49 and 50 in window B D Guinea pig 2bp B D Chicken 637bp Alignment block 50 of 66 in window, 80058690 - 80058690, 1 bps B D Rat c B D Mouse t Prairie vole t B D Guinea pig t B D Rabbit c B D Human t B D Chimp t B D Rhesus t B D Tarsier t B D Dog c B D Panda c B D Cat c B D Cow c B D Opossum g B D Platypus g B D Zebrafish t B D Chicken = B D X. tropicalis - Inserts between block 50 and 51 in window B D Rabbit 2506bp Alignment block 51 of 66 in window, 80058691 - 80058691, 1 bps B D Rat -a B D Mouse -g Prairie vole -g B D Guinea pig -g B D Human -g B D Chimp -g B D Rhesus -g B D Tarsier -g B D Dog -a B D Panda -a B D Cat -g B D Cow -a B D Opossum -a B D Platypus -g B D X. tropicalis -a B D Zebrafish c- B D Rabbit == B D Chicken == Inserts between block 51 and 52 in window B D Dog 1bp B D Panda 2423bp B D Cat 1bp B D Cow 1bp B D Opossum 20bp Alignment block 52 of 66 in window, 80058692 - 80058696, 5 bps B D Rat ttgtc-- B D Mouse ctgtc-- Prairie vole ctggc-- B D Guinea pig caggg-- B D Human ctggg-- B D Chimp ctggg-- B D Rhesus ctggg-- B D Tarsier ctggg-- B D Dog ctggg-- B D Cat ctggc-- B D Cow caggg-- B D Opossum ctggg-- B D Platypus -ccct-- B D X. tropicalis ctatg-- B D Zebrafish --gtgtc B D Rabbit ======= B D Chicken ======= B D Panda ======= Inserts between block 52 and 53 in window B D Zebrafish 3230bp Alignment block 53 of 66 in window, 80058697 - 80058706, 10 bps B D Rat ttgggg---------------------------------aagg B D Mouse ttggggagggctgggtctgggtccgaggggcctgaaggaaagg Prairie vole -tgaggaaggacaggtctgagt-------gcctgaaggaaagg B D Guinea pig tttggg---------------------------------aggg B D Human tcctgg---------------------------------gagg B D Chimp tcctgg---------------------------------gagg B D Rhesus tcctgg---------------------------------gagg B D Tarsier tcttgg---------------------------------gtgg B D Dog tcctgg---------------------------------aagg B D Cat tctcgg---------------------------------aagg B D Cow tctgtg---------------------------------gagg B D Opossum gtgggg---------------------------------ggtg B D Platypus tcgggg---------------------------------gacg B D X. tropicalis ttgata---------------------------------aaa- B D Rabbit =========================================== B D Chicken =========================================== B D Zebrafish =========================================== B D Panda =========================================== Inserts between block 53 and 54 in window B D Cat 4196bp B D Cow 24bp B D Opossum 4bp B D Platypus 88bp Alignment block 54 of 66 in window, 80058707 - 80058707, 1 bps B D Rat t B D Mouse t Prairie vole t B D Guinea pig t B D Human t B D Chimp t B D Rhesus t B D Tarsier g B D Dog t B D Cow t B D Cat = B D Rabbit = B D Opossum = B D Chicken = B D X. tropicalis - B D Zebrafish = B D Platypus = B D Panda = Inserts between block 54 and 55 in window B D Guinea pig 2807bp B D Human 413bp B D Chimp 44bp B D Rhesus 44bp B D Tarsier 23bp Alignment block 55 of 66 in window, 80058708 - 80058713, 6 bps B D Rat catttg B D Mouse cattcc Prairie vole gatacc B D Chimp agctca B D Rhesus agctca B D Tarsier agcccc B D Dog -gttct B D Cow -tacct B D Opossum tcttcc B D X. tropicalis -acttg B D Cat ====== B D Guinea pig ====== B D Rabbit ====== B D Human ====== B D Chicken ====== B D Zebrafish ====== B D Platypus ====== B D Panda ====== Inserts between block 55 and 56 in window B D Dog 2825bp B D Cow 2bp Alignment block 56 of 66 in window, 80058714 - 80058717, 4 bps B D Rat agaa B D Mouse agaa Prairie vole agca B D Chimp aaga B D Rhesus aaga B D Tarsier agtt B D Cow gaaa B D Opossum agaa B D X. tropicalis ggaa B D Cat ==== B D Dog ==== B D Guinea pig ==== B D Rabbit ==== B D Human ==== B D Chicken ==== B D Zebrafish ==== B D Platypus ==== B D Panda ==== Inserts between block 56 and 57 in window B D X. tropicalis 1561bp Alignment block 57 of 66 in window, 80058718 - 80058746, 29 bps B D Rat gaattgtcgtaataaggtggg-------------caaggtga B D Mouse gga------taataaggtggg---------cacacacggtga Prairie vole gcattgtggcagtaagctgga-------------catggtga B D Chimp cagctgtctcagaagcctggggtgtatggccaggcgtggtgg B D Rhesus caggtttctcagacgcctggggtgtatggcccagggtggtgg B D Tarsier ctga--tctgaggagcctgaag-----------atgaggttt B D Cow tatgcgtcataataatatcct-------------ccagaaga B D Opossum ggg------cagttctgtggg-------------catggaac B D Cat ========================================== B D Dog ========================================== B D Guinea pig ========================================== B D Rabbit ========================================== B D Human ========================================== B D Chicken ========================================== B D X. tropicalis ========================================== B D Zebrafish ========================================== B D Platypus ========================================== B D Panda ========================================== Inserts between block 57 and 58 in window B D Cow 211bp Alignment block 58 of 66 in window, 80058747 - 80058779, 33 bps B D Rat caaag-----tgcctttagtctcagcactcaaggggat- B D Mouse caaag-----cacctttaatctcagcactc-ggggaat- Prairie vole caaa--------cacttagtctcatca------------ B D Chimp ctcat------gcctgtaatcccagcactttgggaagg- B D Rhesus ctcat------gcctgtaattccagcactttgggaggc- B D Tarsier ctcaga----agcctgaagtgt--gtac-ctaaaaccc- B D Opossum -----aaaagggactcgtggccctgca----aaggggct B D Cat ======================================= B D Dog ======================================= B D Guinea pig ======================================= B D Rabbit ======================================= B D Cow ======================================= B D Human ======================================= B D Chicken ======================================= B D X. tropicalis ======================================= B D Zebrafish ======================================= B D Platypus ======================================= B D Panda ======================================= Inserts between block 58 and 59 in window B D Opossum 17bp Alignment block 59 of 66 in window, 80058780 - 80058805, 26 bps B D Rat cactgtcagt----------tgga-gccagccagggt B D Mouse cactatgagt----------tggaggccagccagtgt Prairie vole -----tgagt----------tagaggacagcc----- B D Chimp caaggcgggtagatcac---ctgaggtcag---gagt B D Rhesus caaggcgggtggatcac---ctgaggtcag---gagt B D Tarsier caaggtgtgactgtctctcattgccccccg---gtgt B D Cat ===================================== B D Dog ===================================== B D Guinea pig ===================================== B D Rabbit ===================================== B D Cow ===================================== B D Human ===================================== B D Opossum ===================================== B D Chicken ===================================== B D X. tropicalis ===================================== B D Zebrafish ===================================== B D Platypus ===================================== B D Panda ===================================== Inserts between block 59 and 60 in window B D Chimp 17bp B D Rhesus 17bp B D Tarsier 1096bp Alignment block 60 of 66 in window, 80058806 - 80058855, 50 bps B D Rat cacagggcaagac-ccagctagctcaaaaaattagaaagtgggggtgcttg B D Mouse ctcatggcacgac-----ctagctcaaaaatgtagaaagtggcgatgctta Prairie vole ----ctgaacaat-----caaaaataaaaaaccagaaaataggtgcccc-- B D Chimp aaaatggcgaaaccccatctctactaaaaatataaaagccaggcgtggtgg B D Rhesus aacatggtgaaacggcatctctattaaaaatataaaaaccgggcgtggtgg B D Cat =================================================== B D Dog =================================================== B D Guinea pig =================================================== B D Rabbit =================================================== B D Cow =================================================== B D Human =================================================== B D Opossum =================================================== B D Chicken =================================================== B D X. tropicalis =================================================== B D Zebrafish =================================================== B D Platypus =================================================== B D Panda =================================================== B D Tarsier =================================================== Inserts between block 60 and 61 in window B D Chimp 6bp B D Rhesus 163bp Alignment block 61 of 66 in window, 80058856 - 80058863, 8 bps B D Rat gctttttt- B D Mouse accttttt- Prairie vole -cctttta- B D Chimp -cctgtatt B D Cat ========= B D Dog ========= B D Guinea pig ========= B D Rabbit ========= B D Rhesus ========= B D Cow ========= B D Human ========= B D Opossum ========= B D Chicken ========= B D X. tropicalis ========= B D Zebrafish ========= B D Platypus ========= B D Panda ========= B D Tarsier ========= Inserts between block 61 and 62 in window B D Chimp 136bp Alignment block 62 of 66 in window, 80058864 - 80058872, 9 bps B D Rat ttttt---tatc B D Mouse ataatacatatc Prairie vole attgt---tat- B D Cat ============ B D Dog ============ B D Guinea pig ============ B D Rabbit ============ B D Rhesus ============ B D Cow ============ B D Chimp ============ B D Human ============ B D Opossum ============ B D Chicken ============ B D X. tropicalis ============ B D Zebrafish ============ B D Platypus ============ B D Panda ============ B D Tarsier ============ Alignment block 63 of 66 in window, 80058873 - 80058924, 52 bps B D Rat ttatgt------------gtttgggcgttttgtctgcgggtgagtctgtctgtgtactgtggac------ B D Mouse ttacgt------------gtttaggtgttttgtctgcatatgagtctgtatg----ctatggac------ Prairie vole -------------------ttgagacaggatttctctgtgtactcctggctg----tcctggaa------ B D Cow ttatgtgcgtgcatgagggctaagtcgctttagttgtgtctgaatctgtgca-accctatggactgtggc B D Cat ====================================================================== B D Dog ====================================================================== B D Guinea pig ====================================================================== B D Rabbit ====================================================================== B D Rhesus ====================================================================== B D Chimp ====================================================================== B D Human ====================================================================== B D Opossum ====================================================================== B D Chicken ====================================================================== B D X. tropicalis ====================================================================== B D Zebrafish ====================================================================== B D Platypus ====================================================================== B D Panda ====================================================================== B D Tarsier ====================================================================== Rat - Mouse - Prairie vole - Cow c Cat = Dog = Guinea pig = Rabbit = Rhesus = Chimp = Human = Opossum = Chicken = X. tropicalis = Zebrafish = Platypus = Panda = Tarsier = Inserts between block 63 and 64 in window B D Cow 72bp Alignment block 64 of 66 in window, 80058925 - 80058938, 14 bps B D Rat atgtctaatacctt B D Mouse atgtctagt----- Prairie vole ctt----------- B D Cat ============== B D Dog ============== B D Guinea pig ============== B D Rabbit ============== B D Rhesus ============== B D Cow ============== B D Chimp ============== B D Human ============== B D Opossum ============== B D Chicken ============== B D X. tropicalis ============== B D Zebrafish ============== B D Platypus ============== B D Panda ============== B D Tarsier ============== Inserts between block 64 and 65 in window Prairie vole 210bp Alignment block 65 of 66 in window, 80058939 - 80058993, 55 bps B D Rat cagaagtcatcaga--tccccggcaggaggagggacaggaattaagatgtttggttt B D Mouse ----agttatcagaatcccctggcaggaaattggactggaatttcgatatttgattt B D Cat ========================================================= B D Dog ========================================================= B D Guinea pig ========================================================= B D Rabbit ========================================================= B D Rhesus ========================================================= B D Cow ========================================================= B D Chimp ========================================================= B D Human ========================================================= Prairie vole ========================================================= B D Opossum ========================================================= B D Chicken ========================================================= B D X. tropicalis ========================================================= B D Zebrafish ========================================================= B D Platypus ========================================================= B D Panda ========================================================= B D Tarsier ========================================================= Alignment block 66 of 66 in window, 80058994 - 80059139, 146 bps B D Rat gttcctctgtaggccagacatcaatgtcaaatatcttctactgctttctagtttgttttgaggcagggtc B D Mouse gtttatctgtagaccagacatcagtgtcaaatatcttgtattgctttgtagtttgttttgagacagggtc B D Cow gatcctcc-tgacccagggatcgaactcgcatctcttacgtctcctgc------attagcaggcaagttc B D Cat ====================================================================== B D Dog ====================================================================== B D Guinea pig ====================================================================== B D Rabbit ====================================================================== B D Rhesus ====================================================================== B D Chimp ====================================================================== B D Human ====================================================================== Prairie vole ====================================================================== B D Opossum ====================================================================== B D Chicken ====================================================================== B D X. tropicalis ====================================================================== B D Zebrafish ====================================================================== B D Platypus ====================================================================== B D Panda ====================================================================== B D Tarsier ====================================================================== Rat tttaactatgtagcctgggctggctacagatgtagcagaggctaaccttatgcttctgatcctcttgcta Mouse ttt-actatgtagctcgaactggctacagatgtggcagaggctaaccttacacttctaatcctcctgctc Cow ttt-acc-----gctagagccacctg----------ggaagcc--ccctgtcccttta----ccttgctt Cat ====================================================================== Dog ====================================================================== Guinea pig ====================================================================== Rabbit ====================================================================== Rhesus ====================================================================== Chimp ====================================================================== Human ====================================================================== Prairie vole ====================================================================== Opossum ====================================================================== Chicken ====================================================================== X. tropicalis ====================================================================== Zebrafish ====================================================================== Platypus ====================================================================== Panda ====================================================================== Tarsier ====================================================================== Rat cca----tct Mouse cca----tct Cow taatttttct Cat ========== Dog ========== Guinea pig ========== Rabbit ========== Rhesus ========== Chimp ========== Human ========== Prairie vole ========== Opossum ========== Chicken ========== X. tropicalis ========== Zebrafish ========== Platypus ========== Panda ========== Tarsier ==========

Data schema/format description and download

Go to Conservation track controls

Data last updated at UCSC: 2017-01-22

Downloads for data in this track are available:

Multiz alignments (MAF format), and phylogenetic trees
PhyloP conservation (WIG format)
PhastCons conservation (WIG format)

Description

This track shows multiple alignments of 20 species and measurements of evolutionary conservation using two methods (phastCons and phyloP) from the PHAST package, for all 20 species. The multiple alignments were generated using multiz and other tools in the UCSC/Penn State Bioinformatics comparative genomics alignment pipeline. Conserved elements identified by phastCons are also displayed in this track.

PhastCons is a hidden Markov model-based method that estimates the probability that each nucleotide belongs to a conserved element, based on the multiple alignment. It considers not just each individual alignment column, but also its flanking columns. By contrast, phyloP separately measures conservation at individual columns, ignoring the effects of their neighbors. As a consequence, the phyloP plots have a less smooth appearance than the phastCons plots, with more "texture" at individual sites. The two methods have different strengths and weaknesses. PhastCons is sensitive to "runs" of conserved sites, and is therefore effective for picking out conserved elements. PhyloP, on the other hand, is more appropriate for evaluating signatures of selection at particular nucleotides or classes of nucleotides (e.g., third codon positions, or first positions of miRNA target sites).

Another important difference is that phyloP can measure acceleration (faster evolution than expected under neutral drift) as well as conservation (slower than expected evolution). In the phyloP plots, sites predicted to be conserved are assigned positive scores (and shown in blue), while sites predicted to be fast-evolving are assigned negative scores (and shown in red). The absolute values of the scores represent -log p-values under a null hypothesis of neutral evolution. The phastCons scores, by contrast, represent probabilities of negative selection and range between 0 and 1.

Both phastCons and phyloP treat alignment gaps and unaligned nucleotides as missing data, and both were run with the same parameters.

UCSC has repeatmasked and aligned all genome assemblies, and provides all the sequences for download. For genome assemblies not available in the genome browser, there are alternative browser views in the preview genome browser. The species aligned for this track include 20 genome sequences.

Organism Species Release date UCSC
version alignment type

Rat Rattus norvegicus Jul. 2014 (RGSC 6.0/rn6) Jul. 2014 (RGSC 6.0/rn6) reference species

Mouse Mus musculus Dec. 2011 (GRCm38/mm10) Dec. 2011 (GRCm38/mm10) syntenic net

Prairie vole Microtus ochrogaster Oct 2012 (MicOch1.0/micOch1) Oct 2012 (MicOch1.0/micOch1) syntenic net

Guinea pig Cavia porcellus Feb. 2008 (Broad/cavPor3) Feb. 2008 (Broad/cavPor3) syntenic net

Rabbit Oryctolagus cuniculus Apr. 2009 (Broad/oryCun2) Apr. 2009 (Broad/oryCun2) syntenic net

Human Homo sapiens Dec. 2013 (GRCh38/hg38) Dec. 2013 (GRCh38/hg38) syntenic net

Chimp Pan troglodytes May 2016 (Pan_tro 3.0/panTro5) May 2016 (Pan_tro 3.0/panTro5) syntenic net

Rhesus Macaca mulatta Nov. 2015 (BCM Mmul_8.0.1/rheMac8) Nov. 2015 (BCM Mmul_8.0.1/rheMac8) syntenic net

Tarsier Tarsius syrichta Sep. 2013 (Tarsius_syrichta-2.0.1/tarSyr2) Sep. 2013 (Tarsius_syrichta-2.0.1/tarSyr2) reciprocal best net

Dog Canis lupus familiaris Sep. 2011 (Broad CanFam3.1/canFam3) Sep. 2011 (Broad CanFam3.1/canFam3) syntenic net

Panda Ailuropoda melanoleuca Dec. 2009 (BGI-Shenzhen 1.0/ailMel1) Dec. 2009 (BGI-Shenzhen 1.0/ailMel1) reciprocal best net

Cat Felis catus Nov. 2014 (ICGSC Felis_catus_8.0/felCat8) Nov. 2014 (ICGSC Felis_catus_8.0/felCat8) syntenic net

Cow Bos taurus Jun. 2014 (Bos_taurus_UMD_3.1.1/bosTau8) Jun. 2014 (Bos_taurus_UMD_3.1.1/bosTau8) syntenic net

Opossum Monodelphis domestica Oct. 2006 (Broad/monDom5) Oct. 2006 (Broad/monDom5) syntenic net

Platypus Ornithorhynchus anatinus Feb. 2007 (ASM227v2/ornAna2) Feb. 2007 (ASM227v2/ornAna2) MAF net

Chicken Gallus gallus Dec 2015 (Gallus_gallus-5.0/galGal5) Dec 2015 (Gallus_gallus-5.0/galGal5) MAF net

Turkey Meleagris gallopavo Nov. 2014 (Turkey_5.0/melGal5) Nov. 2014 (Turkey_5.0/melGal5) MAF net

X. tropicalis Xenopus tropicalis Sep. 2012 (JGI 7.0/xenTro7) Sep. 2012 (JGI 7.0/xenTro7) MAF net

Zebrafish Danio rerio Sep. 2014 (GRCz10/danRer10) Sep. 2014 (GRCz10/danRer10) MAF net

Elephant shark Callorhinchus milii Dec. 2013 (Callorhinchus_milii-6.1.3/calMil1) Dec. 2013 (Callorhinchus_milii-6.1.3/calMil1) MAF net

Table 1. Genome assemblies included in the 20-way Conservation track.

Display Conventions and Configuration

In full and pack display modes, conservation scores are displayed as a wiggle track (histogram) in which the height reflects the size of the score. The conservation wiggles can be configured in a variety of ways to highlight different aspects of the displayed information. Click the Graph configuration help link for an explanation of the configuration options.

Pairwise alignments of each species to the rat genome are displayed below the conservation histogram as a grayscale density plot (in pack mode) or as a wiggle (in full mode) that indicates alignment quality. In dense display mode, conservation is shown in grayscale using darker values to indicate higher levels of overall conservation as scored by phastCons.

Checkboxes on the track configuration page allow selection of the species to include in the pairwise display. Note that excluding species from the pairwise display does not alter the the conservation score display.

To view detailed information about the alignments at a specific position, zoom the display in to 30,000 or fewer bases, then click on the alignment.

Gap Annotation

The Display chains between alignments configuration option enables display of gaps between alignment blocks in the pairwise alignments in a manner similar to the Chain track display. The following conventions are used:

Single line: No bases in the aligned species. Possibly due to a lineage-specific insertion between the aligned blocks in the rat genome or a lineage-specific deletion between the aligned blocks in the aligning species.
Double line: Aligning species has one or more unalignable bases in the gap region. Possibly due to excessive evolutionary distance between species or independent indels in the region between the aligned blocks in both species.
Pale yellow coloring: Aligning species has Ns in the gap region. Reflects uncertainty in the relationship between the DNA of both species, due to lack of sequence in relevant portions of the aligning species.

Genomic Breaks

Discontinuities in the genomic context (chromosome, scaffold or region) of the aligned DNA in the aligning species are shown as follows:

Vertical blue bar: Represents a discontinuity that persists indefinitely on either side, e.g. a large region of DNA on either side of the bar comes from a different chromosome in the aligned species due to a large scale rearrangement.
Green square brackets: Enclose shorter alignments consisting of DNA from one genomic context in the aligned species nested inside a larger chain of alignments from a different genomic context. The alignment within the brackets may represent a short misalignment, a lineage-specific insertion of a transposon in the rat genome that aligns to a paralogous copy somewhere else in the aligned species, or other similar occurrence.

Base Level

When zoomed-in to the base-level display, the track shows the base composition of each alignment. The numbers and symbols on the Gaps line indicate the lengths of gaps in the rat sequence at those alignment positions relative to the longest non-rat sequence. If there is sufficient space in the display, the size of the gap is shown. If the space is insufficient and the gap size is a multiple of 3, a "*" is displayed; other gap sizes are indicated by "+".

Codon translation is available in base-level display mode if the displayed region is identified as a coding segment. To display this annotation, select the species for translation from the pull-down menu in the Codon Translation configuration section at the top of the page. Then, select one of the following modes:

No codon translation: The gene annotation is not used; the bases are displayed without translation.
Use default species reading frames for translation: The annotations from the genome displayed in the Default species to establish reading frame pull-down menu are used to translate all the aligned species present in the alignment.
Use reading frames for species if available, otherwise no translation: Codon translation is performed only for those species where the region is annotated as protein coding.
Use reading frames for species if available, otherwise use default species: Codon translation is done on those species that are annotated as being protein coding over the aligned region using species-specific annotation; the remaining species are translated using the default species annotation.

Codon translation uses the following gene tracks as the basis for translation, depending on the species chosen (Table 2). Species listed in the row labeled "None" do not have species-specific reading frames for gene translation.

Gene Track Species

UCSC Known Genes Human, Mouse

NCBI RefSeq gene annotations chimp, cow, X. tropicalis

Ensembl genes v86/Oct. 2016 rat, guinea pig, rabbit, rhesus, dog, panda, opossum, chicken, zebrafish

no annotation prairie vole, tarsier, cat, platypus, turkey, elephant shark

Table 2. Gene tracks used for codon translation.

Methods

Pairwise alignments with the Rat genome were generated for each species using lastz from repeat-masked genomic sequence. Pairwise alignments were then linked into chains using a dynamic programming algorithm that finds maximally scoring chains of gapless subsections of the alignments organized in a kd-tree. All pairwise alignment and chaining parameters are the same for all pairs. See also: rat 20-way alignment parameters. High-scoring chains were then placed along the genome, with gaps filled by lower-scoring chains, to produce an alignment net. For more information about the chaining and netting process and parameters for each species, see the description pages for the Chain and Net tracks.

The resulting best-in-genome pairwise alignments were progressively aligned using multiz/autoMZ, following the tree topology diagrammed above, to produce multiple alignments. The multiple alignments were post-processed to add annotations indicating alignment gaps, genomic breaks, and base quality of the component sequences. The annotated multiple alignments, in MAF format, are available for bulk download. An alignment summary table containing an entry for each alignment block in each species was generated to improve track display performance at large scales. Framing tables were constructed to enable visualization of codons in the multiple alignment display.

Phylogenetic Tree Model

Both phastCons and phyloP are phylogenetic methods that rely on a tree model containing the tree topology, branch lengths representing evolutionary distance at neutrally evolving sites, the background distribution of nucleotides, and a substitution rate matrix. The rat tree model for this track was generated using the phyloFit program from the PHAST package (REV model, EM algorithm, medium precision) using multiple alignments of 4-fold degenerate sites extracted from the 20-way alignment (msa_view). The 4d sites were derived from the NCBI RefSeq gene set of Rat, filtered to select single-coverage long transcripts.

PhastCons Conservation

The phastCons program computes conservation scores based on a phylo-HMM, a type of probabilistic model that describes both the process of DNA substitution at each site in a genome and the way this process changes from one site to the next (Felsenstein and Churchill 1996, Yang 1995, Siepel and Haussler 2005). PhastCons uses a two-state phylo-HMM, with a state for conserved regions and a state for non-conserved regions. The value plotted at each site is the posterior probability that the corresponding alignment column was "generated" by the conserved state of the phylo-HMM. These scores reflect the phylogeny (including branch lengths) of the species in question, a continuous-time Markov model of the nucleotide substitution process, and a tendency for conservation levels to be autocorrelated along the genome (i.e., to be similar at adjacent sites). The general reversible (REV) substitution model was used. Unlike many conservation-scoring programs, phastCons does not rely on a sliding window of fixed size; therefore, short highly-conserved regions and long moderately conserved regions can both obtain high scores. More information about phastCons can be found in Siepel et al. 2005.

The phastCons parameters were tuned to produce approximately 70% conserved elements in the Rat NCBI RefSeq gene coding regions. This parameter set (expected-length=45, target-coverage=0.3, rho=0.3) was then used to generate the conservation scoring.

PhyloP Conservation

The phyloP program supports several different methods for computing p-values of conservation or acceleration, for individual nucleotides or larger elements (http://compgen.cshl.edu/phast/). Here it was used to produce separate scores at each base (--wig-scores option), considering all branches of the phylogeny rather than a particular subtree or lineage (i.e., the --subtree option was not used). The scores were computed by performing a likelihood ratio test at each alignment column (--method LRT), and scores for both conservation and acceleration were produced (--mode CONACC).

Conserved Elements

The conserved elements were predicted by running phastCons with the --most-conserved (aka --viterbi) option. The predicted elements are segments of the alignment that are likely to have been "generated" by the conserved state of the phylo-HMM. Each element is assigned a log-odds score equal to its log probability under the conserved model minus its log probability under the non-conserved model. The "score" field associated with this track contains transformed log-odds scores, taking values between 0 and 1000. (The scores are transformed using a monotonic function of the form a * log(x) + b.) The raw log odds scores are retained in the "name" field and can be seen on the details page or in the browser when the track's display mode is set to "pack" or "full".

Credits

This track was created using the following programs:

Alignment tools: lastz (formerly blastz) and multiz by Bob Harris, Minmei Hou, Scott Schwartz and Webb Miller of the Penn State Bioinformatics Group
Chaining and Netting: axtChain, chainNet by Jim Kent at UCSC
Conservation scoring: phastCons, phyloP, phyloFit, tree_doctor, msa_view and other programs in PHAST by Adam Siepel at Cold Spring Harbor Laboratory (original development done at the Haussler lab at UCSC).
MAF Annotation tools: mafAddIRows by Brian Raney, UCSC; mafAddQRows by Richard Burhans, Penn State; genePredToMafFrames by Mark Diekhans, UCSC
Tree image generator: phyloPng by Galt Barber, UCSC
Conservation track display: Kate Rosenbloom, Hiram Clawson (wiggle display), and Brian Raney (gap annotation and codon framing) at UCSC

References

Phylo-HMMs, phastCons, and phyloP:

Felsenstein J, Churchill GA. A Hidden Markov Model approach to variation among sites in rate of evolution. Mol Biol Evol. 1996 Jan;13(1):93-104. PMID: 8583911

Pollard KS, Hubisz MJ, Rosenbloom KR, Siepel A. Detection of nonneutral substitution rates on mammalian phylogenies. Genome Res. 2010 Jan;20(1):110-21. PMID: 19858363; PMC: PMC2798823

Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K, Clawson H, Spieth J, Hillier LW, Richards S, et al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 2005 Aug;15(8):1034-50. PMID: 16024819; PMC: PMC1182216

Siepel A, Haussler D. Phylogenetic Hidden Markov Models. In: Nielsen R, editor. Statistical Methods in Molecular Evolution. New York: Springer; 2005. pp. 325-351.

Yang Z. A space-time process model for the evolution of DNA sequences. Genetics. 1995 Feb;139(2):993-1005. PMID: 7713447; PMC: PMC1206396

Chain/Net:

Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784

Multiz:

Blanchette M, Kent WJ, Riemer C, Elnitski L, Smit AF, Roskin KM, Baertsch R, Rosenbloom K, Clawson H, Green ED, et al. Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res. 2004 Apr;14(4):708-15. PMID: 15060014; PMC: PMC383317

Lastz (formerly Blastz):

Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468

Harris RS. Improved pairwise alignment of genomic DNA. Ph.D. Thesis. Pennsylvania State University, USA. 2007.

Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961

Phylogenetic Tree:

Murphy WJ, Eizirik E, O'Brien SJ, Madsen O, Scally M, Douady CJ, Teeling E, Ryder OA, Stanhope MJ, de Jong WW, Springer MS. Resolution of the early placental mammal radiation using Bayesian phylogenetics. Science. 2001 Dec 14;294(5550):2348-51. PMID: 11743200